Good points, of course, BW.
I don't have a magic answer, but having played every cRPG since Akallabeth on my Apple][+ I do have a few ideas.
Firstly, I would suggest that skills that are so fundamental that everyone needs them are almost pointless, since there is no real choice but to invest in them. Cartography comes to mind. Everyone needs a mini-map. Forcing people to burn skill points there doesn't make a lot of sense to me.
Next, take something like lockpicking. Go ahead and try and convince an old-school player that he doesn't really have to open every chest in the game. Oh, right. Now, you do provide tedious ways for mages and fighters who don't want to invest in lockpicking a way to get open locked items, but it is so tedious, that it borders on not really being an option. The option should be less efficient than a thief who invest on lockpicking, but perhaps by not so many orders of magnitude.
But the killer is combat... very hard to find a way to create multiple viable ways of killing stuff.
Regardless, I think your fundamental challenge of how to create a fun RPG system is greatly impeded by the fact that you want it to be a solo char. A solo char is, by nature, going to need to be a bit of a jack-of-all trades, unless you are really building your game with having multiple playthoughs be mandatory to see a good percentage of the content you are creating.
The fact is, though, the way the old "old school" games (Wizardry, Bard's Tale, Ultima 5-7, Might and Magic, Magic Candle, etc) solved this problem was by having a party. A party dynamic allows for much greater variety in how you tackle the game.
Some people will go with the classic, 2 fighters, 1 thief, 1 mage, 1 cleric kind of deal. Someone else though might go for 4 mages and a thief, with one mage focusing on alchemy for healing potions.
Yet another may go for no magic users at all, and use archers for ranged damage, and again resort to alchemy or first aid for healing.
The old school games that built solo players (Ultima 1-3, 8 & 9, Ultima Underworld, Arena, etc) all understood that by nature you need a jack-of-all trades, thus limiting the options that players could truly choose. All they could do is, in effect, create the illusion of choice.
I know you aren't planning on making a party based game quite yet, but I think that heavy investment in mechanics for a single char game will have a limited ROI due to the need to have a bunch of critical skills, and so the issue boils down to "am I going to do most of my damage via magic, melee or ranged".... but all utility skills are going to be necessary no matter what.