Okay here's a step-by-step review of your thoughts ...
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1. Purchase Software Development
I think the main problem of the gameplay - as many of you allready stated - is the lack of gameplay challenge once the arc/arunmore mission are completed. While the other problem is to get good advanced software upgrades (i.e. bypasses) I thought it would be nice, if one could spend parts of his bankhack money to develop the software he has. Something like independent research labs. You register, you copy the software you want evolved up to them, and over the time you get leveld up software.
The problem with the software developing would be that there is only a limited set of features for each of the different tools that makes sense. Though there are some that could be updated as security mechanisms get better over time (eg the bypassers, decypher, etc.). However though it may appear good to some people doing something like that wouldn't change nothing about an advanced game losing it's appeal over time (since after all you still hack the very same machines, do the very same stuff, etc.).
Okay we're talking over-time unlocking of already implemented and balanced ingame content? Well why not (for the "why" read the gateway comment) . Wouldn't change much, but would at least make the start of the game a bit tougher and increase the value of the different versions of the very same tool. I personally always just bought the newest shit of the list and skipped any previous versions (and I know that most people will probably do it that way). Why pay twice for something you can have for a few more credits too if you did a tad more missions? From the game designers point of view the different versions being so close to each other feature- and price-wise simply doesn't have much sense in it. Eg why bother getting a Trace Tracker v2 for 600 if you can get the real thing with even an accurate time estimate for just a few houndred more (meaning even in worst case just one more mission-accomplished already is enough)? The version improvements are good the way they are, but each new version renders the prior one useless and therefor just replaces one piece of content with another instead of enhancing it's overall variety.
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2. Found your own labs
As there are a couple of good software engineers in the academic database, why not blackmail them with some crime they didn't commit and force them to work for yourself. They could develop the software you need! In general I want to make my own servers and so, why not make up your own research laboratory - your own public accsess servers and so on?
See the above comment ... period.
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3. Make the gateway upgrades less accessible.
It's a bit boring, that you can upgrade your gateways right up to the max, once you hacked a bank. As there is a progress in software development, there should be one in hardware development too. Maybe combined with some missions. Something like stealing the blueprint for a new gateway from one company - and once the employee has it, buy the next generation of gateways from that company.
I actually thought about that one a few as well since it would definately have an impact on the gameplay at least for those in need of a better gateway than the standard Alpha to do some serious bank hacking. The game is pretty much too money dependant, although money is something you can amass rather simply in the game.
However the catch is that once the Feds kicked your butt the game starts anew and all parameters are reset. Meaning you would end up having to wait for that cool spiffy gateway of yours to get back to where you were busted ... that's called the elevator problem in game design: You pull the switch and the elevator comes down (down-time) you have to wait for it reaching the level you want to get to (down-time). You accidently fall of the elevator hence you have to wait for it to reach the level you wanted and come back down just to wait for it to get back up again .... so all in all you'll end up having to wait for somthing and since waiting is no fun at all implementing elevators just to have them is just incredibly bad game design and proof of the designer never having played that part himself.
However since skilled player won't face total annihilation often anyways it appears that shouldn't be too much of an issue anyways.
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4. Get style upgrades.
There should be companies on the map selling stylistic upgrades for your huds, software tree, and all the look of your game. I like all that customized stuff in the other games out there (like NFS Underground, Tiger Woods....). Its way cool to get all these things and It keeps you playing!
Um ... what? ... No not really. One word: content-driven ... far off course. Get back on track agent!
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5. The bypass enhencer
This is just a small change I thought abaout. Instead of moving all the bypasses over the correct symbols in the HUDConnection Analyser, why not insert a new software, which automaticly patches all the bypasses you have.
Just one word: WORD! You actually hit the nail on the hat here. Having to move those bypassers by hand every time you have to reconnect to a LAN after being kicked off by an admin is pretty damn lame ...
Nuff said.