I'm afraid I haven't played 2ed in so long, I don't recall the details of how the classes work, so I can't help you decide how you want to present the class tables to the user.
The second part of your reasons - the level dependant abilities - that could be handled either way - that's not a reason to pick the way the Pathfinder/d20 files choose classes and levels vs. the way the 4ed files choose class and level. Differing HP and other rolled values at each level is a legitimate reason to have separate picks for each level, but you should also consider other ways to go about that.
How about choosing each class, and choosing the level of each one with an incrementer, and then a set of 20 (or more) bootstrapped picks reveal themselves as you level, each one offering the HP box for that new level?
How about a set of universal class level picks - the same 20 (or more) picks would be enmassed to all characters. The actual classes would be added once each, with an incrementer, and the level picks would reveal themselves as you leveled. Each one would figure out what level it represented, so if it calculated that it was for a Fighter level, it would ask you to enter Fighter HP. If it was for a Fighter/Thief level, it would show you a Fighter HP box, a Thief HP box, and have you enter each, and then show you the total for that level.