[Coyote]

As you say, they ARE a good mechanical bonus and the mechanical disadvantage is usually somewhat minor.  So let me rephrase my question:  How many players do you see take totems Mentor Spirits because they want to explore roleplaying a hermetic mage who filters his view of magic through the lens of a primal spirit and lives by its guidance, vs how many go "Oooh, five karma for bonus dice, shiny!"   

I do see players taking Shamans and caring much about what "totem" they follow. I do not see players taking Hermetics and caring that much about what their mentor spirits say. By "that much", I mean that they do the minimum required to keep their mentors happy, and after that do what they want. However, I think that's quite reasonable for the Hermetic tradition vs the Shamanic tradition, given that the Hermetic TELLS spirits what to do, and the Shaman ASKS spirits what to do. So the Hermetic mage is going to give less weight to the advice and interests of his mentor spirit than the Shaman. So, it follows that players take Hermetics will less of a care for what their spirit's guidance may be, than a Shaman.

[Mirikon]

One does not 'choose' a mentor/totem. One doesn't choose to be loyal because of Dog. Dog comes to those who are loyal. In the end, Mentors are like the distilled essence of a mage's personality. Shark comes to fighters. Seducer comes to lovers. Dragonslayer comes to warriors. And so on.

I admit that my magic types often have a mentor, but that mentor is always a reflection of their character. Saying that they are 'less interesting' than a mage without a mentor is highly subjective.

Now, as for hermetics that are still played like they were back in 1-3E? Maybe. Just looking at the Jackpoint list, there's at least one of those style hermetics on the board. But he's been around for a while. New characters are generally in the new thinking.

[Blue Rose]

One does not 'choose' a mentor/totem. One doesn't choose to be loyal because of Dog. Dog comes to those who are loyal. In the end, Mentors are like the distilled essence of a mage's personality. Shark comes to fighters. Seducer comes to lovers. Dragonslayer comes to warriors. And so on.

I'd say that would vary pretty wildly.

Sometime, your mentor comes to you because you are of like mind.  Sometimes, your mentor comes to you because they believe you are misguided and need to be set on the path and are not beyond hope, possibly even forcing that guidance upon you.  Sometimes, in a moment of need, you go seeking guidance or power, and you find it, whether that be in the place that is right in a spiritual and fulfilling sense or in a manner that is anathema and forces you into spiritual instability.  Sometimes, the mentor will treat you like prey.  Sometimes, you will hunt the mentor and exploit its power.

It varies wildly.

The mentors and their relationship to the world are vague and nebulous and variable from person to person and belief to belief.

[Sterling]

One does not 'choose' a mentor/totem. One doesn't choose to be loyal because of Dog. Dog comes to those who are loyal. In the end, Mentors are like the distilled essence of a mage's personality. Shark comes to fighters. Seducer comes to lovers. Dragonslayer comes to warriors. And so on.

I admit that my magic types often have a mentor, but that mentor is always a reflection of their character. Saying that they are 'less interesting' than a mage without a mentor is highly subjective.

Now, as for hermetics that are still played like they were back in 1-3E? Maybe. Just looking at the Jackpoint list, there's at least one of those style hermetics on the board. But he's been around for a while. New characters are generally in the new thinking.

If a Mentor Spirit is taken for story purposes then that's wonderful.  It's when Mentors get chosen because they provide the best buff that I have an issue.  Especially when the player ignores the downside.

As an example I'll point at Maverick in the Arcology Podcast.  He's a Mystic Adept with the Eagle Mentor, because of the bonus to Perception.  Not only has the allergy to pollutants never come up, but the character smokes cigars!  At my table he'd be looking at dice pool penalties right there!

An Hermetic with a Mentor that furthers the story is just as interesting as the Hermetic who stubbornly sticks to the old ways.  It's the one who built the character as a dice pool who is boring.

[Blue Rose]

Maverick has a mentor? O.o

[Fizzygoo]

"Mentor spirit? Yeah, I've got a mentor spirit. It's called drain."
- Freshman Hermetic Studies student, MIT&T

I prefer playing hermetic-leaning no-mentor-spirit mages when I play magicians. Since I tend to gravitate to jack-of-all-trades type of characters and played earlier SR editions, the idea of playing with a mentor spirit comes with "constrictions" (disadvantages) and thematically they are still, in my mind, a huge social and mental commitment for the character. But if I ever get an idea for a character with a mentor spirit, I'll dive right in.

In general, I don't like the way Mentor Spirit disadvantages are not uniform:
  Dragonslayer: Don't break a promise - under the Player's control.
  Eagle: Allergy (pollutants, mild) - under the GM's control.
  Rat: Test to flee combat - under the Dice's control.

I'd prefer they all be the same (player's, GM, or Dice's control) or staged disadvantages for each (if you choose a player's control for the disadvantage then you get less bonuses on the advantages than had you chosen Dice and more if you choose under GM control, for example).

As for the second part to the OP, how often do the disadvantages rear their ugly heads in the campaign:

In our group we have a Bear shaman, an Eagle adept, and the no-mentor-spirit Hermetic/Black Magic mage.

We've played 47 sessions so far (14 missions). Last night was the first time hitting the Eagle adept with pollutants (largely the GM's [my] fault for not bringing it up previously, and even in the last session the Bear shaman said "here's a rating 6 respirator" which I allowed to alleviate the allergy [they were in the Rats' Nest in the Redmond Barrens]...but today in going over it I couldn't find anything on respirators helping with the Allergy Negative Quality. So, unless I find something that says different, I'm planning on telling the player that in the Barrens in general the respirator will alleviate the allergies, but in high pollution areas like the Rats' Nest it's not just respiratory in nature [hives, watering eyes, etc.]).

The Bear shaman on the other hand has done real well at avoiding combat, using her Beast spirit in her place, and not taking damage. But the thing I've kept forgetting is that the disadvantage includes people under her care taking damage. Of course I can chalk that up to the vague wording of "...or if someone under your care is badly injured." Is that one box of physical, 3, 6? Perception check if ally gets knock unconscious via stun and on a failure to realize it's stun then check to go berserk?

So...not as much as they probably should.

[Longshot23]

I rebuilt SR3 characters in first SR4/A, then SR5. One of them was the SR3 Street Mage, which never seemed anything other than hermetic (remember, SR3).

Admittedly she's never been actually played, so I have no idea how well or badly the character build would do. It's a minor point of interest that, although the Street Shaman continued through the editions, the base Street Mage seems to have been chopped.

[Nightmare]

Same thing with the Former Wage Mage and the Burned Out Mage...they've both dissappeared along with the Street Mage. And the Wage Mage was a definite hermatic with heavy leanings on logic casting and science/formuli ideas.

[Rosa]

As for the archetypes that have disappeared. Thats probably just Down to Space in the books and honestly if you have the street shaman in the book, you can easily modify that one to get a traditional street mage instead.

The World of Shadowrun has been through about 65 years of magical R&D, it would be very strange if the magical paradigms hadn't changed at all in all that time, i actually rather like that they have, it makes the World more dynamic.

As for the hermetics and mentor spirits, i find that the section in Street Grimoire called "The nature of spirits" is actually pretty good as it also covers various theories as to what spirits are and where they come from. Some of those views are very hermetic in their flavour.

As others have said it's on the GM to make sure that the players formulate just what their relationship to their mentors are and i would add just how they see mentors generally, and of course it's up to the GM to make sure that the players actually feel the downside to having a mentor. Besides that your mentor should also influence...how you deal with other spirits, which spells you learn, which metamagical techniques you learn....etc. So there's plenty of potential for good roleplaying in having a mentor even for a traditional hermetic, but i agree that it should never ever just be a quick inexpensive way to get some bonus dice, but as said that's very much on the GM's head, and also to explain to the player what having a mentor will mean in their game.