I fully agree with your post. When I edit a (current) 25 man roster I touch nearly all of the player ratings. I made a excel sheet and compare the (split) stats of the players to it and then assign ratings. I don't do this in a 100% accurate way, but I use a step system (5, 10 and 15 points) to edit the ratings because otherwise I never would be able to complete anything. 2k hasn't used a very deep system as far as I can tell. Many (split) ratings are simply off. It seems that they mainly looked to assign certain ratings to players hence these players should get a particular OVR.
Regarding my system:
E.g. when a player has a batting average against LHP of 26% in real life this would be a rating of 69 in my excel sheet. Now it depends on what the game has given the player. If he is rated way above this rating (for whatsoever reason), e.g. rated 82 contact vs. LHP, I do not give him exactly 69, I lower the rating by 10 points so that he becomes a 72 contact vs. LHP rated batter. My eyes and fingers react somehow faster with this method, I can't tell ya why.
But it seems to be easier to work in those steps than to put in a certain number all the ****ing time.
This system is used for nearly all ratings: contact for pitchers and batters, power or homerun ratings, the eye rating (OBP), and so on. I also edited many pitch types and gave them not only new ratings but also assigned them real life pitch speeds. I did touch the tendencies for both position players and pitchers, too.
IMO it helps the game a lot. Not only that the OVRs aren't messed up (IMO they NOW represent way more a players value than before) like one could think, but also the game plays (at least slightly) different. Now you can't put in a power bat and expect him to hit bombs no matter if he is against a RHP or a LHP. Put in Kendrys Morales against a RHP and he will shine, put him in against a LHP and he will suck. Simply like in reality. That is how I think it should work.
The only problem is that the adjustments need a big amount of time, especially for pitchers and their pitches since you have to switch all the time between the game, the editor and your browser. For editing the current 25 man roster (13 position players and 12 pitchers) of one MLB team it takes me somewhere to between 2 and 3 hours.
For some time past fangraphs.com has become my best friend, I can tell ya. But comparing the real life stats to 2k's ratings makes me wanna scream, really...
For the problem you stated regarding the groundballs I didn't find a proper solution yet, but changing the contact and power ratings and working on the batter's and pitcher's tendencies did help more than a drop.
EDIT:
Ah and I nearly forgot to state this but I think too many people put too much value into OVR ratings. What should matter are the certain fielding stats and the other parameters. But not mainly the OVR. You can easily create players with high OVR by simply giving them a high speed rating an moderate batting ratings. Would such a player in reality be considered as a way above average or even supreme guy? No he wouldn't. he simply would be a decent batter with a bunch of speed. You should have to look deep into the details and decide what you want to do with a player. And not only pick up a guy because he has a good OVR. When you need power against a LHP because your lineup lacks it you should search for a batter that has power against LHP. Searching for a player that only has OVR power shouldn't be enough IMO. As far as I remember 2k stated exactly this in some developer's diaries. But they never implented it in detail.
But I think this a simply an approach that doesn't fit with the mainstream. The most people (and of course they have the very right to!) simply want to start a game and play it. Hit a bunch, throw some Ks. However since I am very deep into baseball and watching way more games lately than previous times this isn't enough for me anymore.