A few ideas..

[Devorock]

First have a option for defrag to send files to the END of ur memery..
why? because i find it much faster to move my programs to the end that way when i'm copying files i don't have to scroll down but can start at the very top.
Second make money transfers smaller taking the cash from 1 transfer trace mission leaves me with more then enuff cash to get all software+a maxed Trinity.
add more official gateways, when i buy a custom gateway in FBI mod it works fine i've found until i restart the mod then it can't see the gateway so it crashes being able to get Trinity so fast then not having anything to upgrade later makes the game a little dull.
Also on gateways.. maybe limit the Processor power Memory and Gateways to Uplink Rank and or the Neuromancer rating..
Maybe have mission offers more closely tied to the rating..
Maybe other rewards for missions such as different Gateways unlockable from missions, or some kinds of softwares become buyable or you get them as rewards after certain missions.

[FrostShard]

You've got a few good ideas there (I like the defrag thing) but if you find that stealing the sums of money you get in the transfer trace missions makes things too easy, then... uhh... don't steal it?

[abigbagofcrap]

twould be no fun without stealing massive amounts of money from a bank . They brought it upon themselves, charging me $500 for an overdrawn account.