Generally I totally support your sentiment. I don't think 3 is a big deal, probably not worth the time it would take to revamp all that and starting at level 3 would just demolish non-D&D players. As many others have said, alignment doesn't play almost any mechanical role in 5E, so I'm happy to have it just for RP purposes.
All that said, there are certainly some aspects of tabletop D&D that can be done much better in a cRPG (like stealth/hiding, which in PnP is very flexible and DM dependent because it's too complicated for basic rules (think light, sound, lack of facing, etc)). So there are some parts of D&D that I'm okay with them altering a bit. But at this point it feels like they've over altered just to use mechanics they had from DOS2.