In theory it may lead to more diverse players picked, but you can also look at it and say it highly dissuades anyone from picking players who don't get a lot of hits. Karnage and Reencarnacion would be the only viable top-tier forwards. No one would take a McJustice, Koponen, or Molholt over either of those two. I actually think how it is now makes people think more about their decision, rather than just picking players who get a ton of hits. It's definitely not perfect, though, and the scoring for hits and PIMs is definitely something I was always concerned with when I was running it.
At least, I don't think entirely getting rid of PIMs and leaving hits at their current value is wise. Perhaps making PIMs worth less (as in a smaller negative value) or disregarding them and making hits worth less would work. I think a change would be fine, of course. I never considered it something that necessarily needed to change, because everyone is playing under the same rules, but some alteration could definitely be for the better