I don't see the new character progression system as being gimped in any way. Everything is there, just that the way you bump up skills and stats is done differently. Now, rather than have a load of points to manually distribute for tiny increments across your SPECIAL and skills, and taking perks that were useful but comparatively not as potent as they are now FO4, you have the perks significantly powered up and tied to your base SPECIAL stats and gated by level. The only streamlining I see there is that what you used to have to accomplish with three different steps (raise Special, raise skills, select perks) is now accomplished in one (assign one point per level to either SPECIAL or a perk).
Yes, you had more flexibility to manually allocate skills for very particular combinations of skills, but apart from the oddball stealth/big guns type build, which is arguably gimped because of what you had to give up to make that character, most of the time you were manually raising related skills and taking perks to support a playstyle or create a particular specialized build. This is exactly what the new system helps you do but without having to allocate a mess of points to the specific skills that are now associated more generally under their respective SPECIAL category or perk cluster.
I DO take issue with the (so far, in my playthrough) apparent lack of application for some skills outside of combat. Everyone mentions conversations and only Charisma having any effect and I agree with that. Others I'm still not sure of but might work out. What used to be the skills Science, Repair and Medicine are now all under intelligence as perks, and I have already begun to see cases where having upped those skills is paying off, even outside of combat. I don't want to elaborate much because spoilers. Also Lockpicking obviously has an effect in-world.
Ultimately, though, I keep coming back to this: apart from stat checks and some extra conversation options, how much of an effect did all those individual skills really have that they don't have now? There were tons of cases in previous games where you could alter conversations by passing checks on any of four or five possible skills in one conversation. How meaningful is that really?