we now have to "waste" 12 points on aptitudes to get skills on lvl3. It's especially annoying if you want to pick skills from all skill groups and not just heavily invest in one. Feels a bit constricting.
you're by no means the only one to think so, but that's actually intentional: getting rank 3 in all 4 aptitudes is not meant to be the ideal way to spend your points. you're supposed to think about how you want to specialize, instead of always getting all the best skills from every aptitude. that is also why the aptitudes themselves do not offer any bonuses anymore.
this system has two advantages:
1) there will be more variety between different campaign runs (at least assuming you don't always specialize in the same thing in all runs).
2) individual skill balance is much easier to get right, since even a really powerful skill might not be worth taking if you didn't intend to grab several other skills in its aptitude as well. having a skill that is a no-brainer
within its aptitude is much less problematic than one you'll
always want to pick up.
the downside is that, as you say, the system feels constricting, and spending a point on something that doesn't by itself give any bonuses whatsoever isn't satisfying either. rather, that point is an investment into future bonuses.