I am not sure why you're apologizing as I think it's great to get a look at the methodology. Thank you. What you said sounds pretty good to me. I agree with much of what you said. In the case of 500k players they are quite popular/optimal as backups and generally speaking they're not very impressive offensively so while your point is valid about them costing your team plate appearances I would argue that this is the norm until the salary starts to increase.
I still believe Molina and Wesley are superior as many of the 500k players are quite lackluster (and rightfully so). I do think it's fun to hunt for hidden gems and there are many good examples of well balanced but useful 500k players. I think things start to break down quickly when certain cards are compared. I'm not sure why it is the case but many cards have few if any redeeming qualities. For example: Let's compare Bengie Molina to clarkson Brazelton.
Molina wins in: defense rating, arm, t-split, passed balls, fewer strikeouts (none), singles, doubles, homeruns, OBP, BA
Brazelton wins in: double plays (impactful),clutch
I don't see why anyone would ever take Brazelton unless it was for a theme league or a favorite player or something like that. He seems completely atrocious to me. There are lots of cards like that in the game and this is why I feel more updates with pricing would be good. In the case of 500k players I assume you're not going to enhance their card values so I feel it would be best to either remove them or replace them with other options. Molina IMO should cost more than 500k if cards like Brazelton cost 500k. Without looking I am confident it would be easy to find 550k+ cards that are weaker than Molina by a significant margin.
I could look at Wesley if you want but I've been rightfully accused of lost posts
Instead, I'll just suggest you look at Ed Goodson. It doesn't get much worse than that!