Random is probably the best way forward as it would probably keep the game 'fresh' for everyone involved. Though, granted how the game is, you can probably set it up so that you can fit your needs. Heck, house rules would probably remedy it. Though, granted, I know some people would rather play the game as intended.
-Smaller floors: Self-explanatory on how this would help you getting into the top floor.
-Starting on the top floor: My friend who played this with me when I bought this suggested this as we were "the worst hackers ever", rarely ever getting more than 2 rooms from the second floor. Flavor-wise, all the operatives were dropped off on the rooftop (and the building has the best stuff built on top) and must escape through the bottom (floor). For some reason, we didn't like the labyrinth suggestion of shuffling the blue and yellow floors together as much.
-Extend the proximity limit: Since my games tend to have horrible luck, even when we start the game off at -1 alarm (we last had the Surveillance Room as the entry point, followed by Security Station). As you can tell, we'd be hitting 100 too soon. So what we're planning is to do this. Play the game as normal, but as soon as 100 is hit, instead of ending the game right there, increase the Alarm if possible, then continue for another 100.
-An elevator: One time only and only from the first (beginning) floor, when an operative choose to play his Advance card, he may use the elevator. He/she rolls the die and will appear on the corresponding room of the second floor. For example, rolling a 6 would place him at the deepest room while rolling a 3 would place him at the 3rd room of the second floor. Alarm increases by 1 (elevators have cameras, don't they?). The operative will also be delayed.
Maybe we should just start a "house rules" thread and see what ends up being popular (if any). Personally, I'd like to see blanks being offered since my friend and I have some ideas we'd like to play out.