In the broader picture...it's not the home runs. It's the engine. I'm pretty sure I'm not the only player here that signed up for a somewhat realistic baseball related game. If the developers need to tweak the engine to try to make results match what the ratings dictate they should be, more power to 'em.
Swamp, if you want to take players like Gorman Thomas who in his best season hit 45 home runs and base your team around players like that, you'll continue to see results that disappoint you. You would probably bypass a player like his own teammate of that same season who hit "only" 28 home runs, yet in the same season, with 100 less plate appearances created as money runs as Thomas did.
The point of the comparison is that while Thomas created a nice 6.6 RC/27, which is production you'd like to have, all of it depended on power. Sixto Lezcano, on the other hand, had pretty good power, but created 8.8 RC/27 and was a much more valuable player that season.
When the sim engine is tweaked to make the game more realistic, the idea is that you'll survive that if you concentrate on having good players not one-dimensional ones. And that's how it should be.