I'd like to chime in here, a bit late, but I hope that is OK.
A lot of the stuff that was put in to the old TT games was due to the design constraints and the nature of the medium (d6 dice, rulers, and generally immature kids arguing "I could totally jump that far in that situation!!!1!!" or "No way, that grenade would still totally hit you! You think shrapnel doesn't fly that far?!?!"). With the video game mechanics, a lot of that can be handled differently. Is it better? Probably, but it will certainly feel the same.
Regarding the skills and random vs planned, there's no reason it can't be both. The players playing aren't each individual ganger. If anything, the player is more the leader, ordering his subordinates. So progression and leveling up doesn't have to be completely planned by the player. However, a leader can certainly choose to order their underlings to study, practice, or focus on skillsets. So do both.
Have a certain percentage of random character development skill-ups occur without user input. These are traits that the ganger discovers they are good at, have an aptitude for, etc. Because they can be handled this way, you don't need any training time for them. They just happen.
You can also have planned skill training similar to Mordheim. Send your ganger or juve off to train in some skill, it costs financial resources, and some measure of time. You may find yourself trying to train to their strengths that they've already discovered "organically" to maximize benefits, and thus giving yourself a bit of a character arc for a guy that was collaborative story-telling between the player and the game, and not just something from the players initiative.
You can actually do the same thing even with the Mordheim skill system. In Necromunda, when you rolled, you either got attribute A or attribute B most times. You can do the same thing, but still give the player choice. Have the randomness on the random attribute gains be in the category (physical, martial, mental, etc) and then let the player pick the exact distribution (leadership, weapon skill, etc). Some attribute level-ups could be random, some planned. Maybe one random increase per level, and one planned?