I think the drafts in level 2 and NBBA should be different than lower leagues. The players should be better or at least have higher potential for training purposes. I agree, I had the most fun in lower leagues where you could start a good draftee, or at least play him while training. You could win with a run and gun team in lower leagues too. I think they tried to capture that new team feeling with Utopia.
I will agree on some of the points. The inside game is definitely overpowered vs. the outside game here, and it's definitely easier to assemble a strong LI clone than create a team for other tactics. But Silverbacks is the example that proves it can be done - they won the NBBA and the tournament running motion. That's one of the reasons why I've been relatively disappointed with GDP - my hope initially was to see how far I could go with a team almost always running Princeton, but the GDP on top of the 3-2 zone just makes that impossible.
I think the draft should be independent of league level, but definitely should include some older players with much higher skill levels - things like 15-20k salary range guys with decent skill distributions, but capped (and probably at age 23). It would be a nice alternative for teams that aren't finishing low enough to look for a highly valuable 18yo in the draft and couldn't train one if a decent one fell to them. I haven't done anything other than randomly arrange players in my draft list for a while - every time I've promoted I figured that was the end of my run and I'd be drafting high, and it hasn't happened yet.