The Skill thing isn’t necessarily an issue. Even the SRD under https://www.5esrd.com/gamemastering/5th-edition-options/ has a section for “Variant Skill List”. Alternately you might consider just stating that the lifepath generated at a certain point gives you “skill in blah-blah, which give you Proficiency in Athletics”, or whatever is appropriate. Per standard rules if you get Proficiency (or a Tool, don’t forget you have those as well) a second time it just means you get to choose a Proficiency (or Tool, if it’s a Tool) in its place. I’ve mentioned before (I think in that thread) that my concern with lifepath generators is if they constrain a player too much then they can be problematic so having situations arise where a character might already have a Tool Proficiency of, say, Smith’s Tools because of an apprenticeship, or something, but then ended up with, I don’t know, a merchant thing that would give them the same tools for some reason, then letting them say “You know what, since I already knew smithing and had those tools, during that time I actually took the opportunity to learn some of the Masons art!” and get that as a Tool Proficiency seems just as good, IMHO.
And definitely don’t forget that while Skill Proficiencies are broad and seemingly limited, all of those Tool Proficiencies are where a lot of the old “Skills” actually went to! So you definitely still have all of that flexibility there.
I think the difference is you’re effectively creating a more granular version of the standard “Backgrounds” system is all, IMHO. Nothing wrong with that at all, I don’t think, especially if you use that to kind of make up for the whole BaB disconnect, if you will.
I largely do agree that the Martial Feats need to stay, however. I’d probably suggest that, like they are for the 3.5e version, they should be an add-on to the Feats system and not integrated directly into it anyway. And that should cover it. After all the main thing to consider is always balance and as long as both the players and the NPCs they face are using the same system then you naturally have that largely built in, so I don’t think it would be a problem.