Both 3.5e and 5e have their merits. Assuming Larian actually implements the rest of the PHB for 5e (and continues to do their adjustments for video games), I actually prefer the 5e system as a base.
3.5e has more customization decisions, but most of the mechanics scales terribly.
5e has more limited customization decisions, but Larian seems to be actively going out of their way to add more to the game - i.e. weapon special attacks etc. I think if they activated rolling stats or a higher point buy, that might encourage people to pick up more feats to solve that issue.
I feel like at the very least, the 5e classes have far more identity. And multi-classing casting is a joy in 5e.
Not sure how they can fix skills, but I didn't love the 3.5e skills mechanic either. Its dependency on INT and hyper-specialization had its own issues.