There are lots of moving parts to this question, so it's pretty easy to go from a question of strict nuyen cost to one of character generation and opportunity costs.
I think cyberdecks should be the best tool out there when it comes to doing illegal things on the Matrix. Yes, you may be able to cobble together something that can approximate some of a deck's functionality, but a deck should be the standard. With that in mind, I don't mind their current costs. They could be a little lower, so as to allow a decker to expand non-decking elements of his character a bit, but I don't think people generally hate the idea that deckers are Resource A characters most of the time. The problem isn't one of initial cost, it's one of in-play upgrading. One of the underlying principles of Shadowrun is "earn money and buy improvements." Deckers plateau for long periods of time--often entire campaigns--which can be frustrating as a player who is forced to watch his companions show off new toys every other run. Throw enough money at the group so the decker can buy a replacement and you've suddenly thrown off the power curve for the mage's foci and the sam's chrome.
The build-from-scratch rules of previous editions were popular, but build-from-scratch rules (for anything, in many RPG systems) always seem to have a blindspot that turns it into its own minigame. Win the minigame and you win the bigger game. Since I want a diversity of good options in order to encourage differentiation among characters, that's not an especially fun prospect.
So with that said, I'd like to see more rules for upgrading existing cyberdecks. There's some of this in Data Trails, but I'd like to see more and have it be cyberdeck-only. Between the current modification rules and positive qualities, it's actually not that hard to get next tier performance out of a deck. Ideally, the customization would encourage specific approaches to decking. Right now, there's an army of Perfect Time, Overclock, Codeslinger (Hack on the Fly) deckers who all operate in generally the same way. It's effective, so I can't really blame them. What if I added something that made Brute Force more interesting? Not simply a +DV thing, but something that a player could develop a tactic around? I'm not nerfing the all-Sleaze-all-the-time approach, but I'm making other options as good, just in different ways.