The LPTV station doesn't count against station ownership, which is why they're allowed to keep it.
James Spann has
commented on the situation on his Google+ page and he basically says he expects little to change for the end user (viewer) unless you're OTA. Those people will have to do a re-scan of course to pick up the new channel assignments.
As far as how Sinclair runs things, I can offer some observations from the Mobile-Pensacola TV market, where Sinclair controls four TV stations. Sinclair owns outright WEAR-3 (ABC) and WFGX-35 (MNT). Deerfield Media owns WPMI-15 (NBC) and WJTC-44 (Ind.) but LMA's both to Sinclair. Of course with the new rules in place this agreement is grandfathered in.
Sinclair has made reasonable improvements to WEAR in the years I've lived here. Their set is modern and they have a decent roster of reporters, along with some popular long-lasting anchors. But that station primarily covers Pensacola so I don't watch it much. It's a little more low key and laid back in style than the Mobile news programs, IMHO. They run just one subchannel, 3.2 carries ZUUS Country (which I understand Birmingham just lost recently.)
WFGX is your typical My Network TV affiliate and is pretty indistinguishable from WABM except that WFGX also carries some This! TV programming in the mornings. It also has just one subchannel, which just came on this month with the Sony-backed getTV network. WFGX also carries a live 9pm edition of WEAR news, something they added in the last year or so.
WPMI is the perennial last place news station in this market but is the one I watch most because I think they have a good mix of personalities for such a small market. Most people watch Fox 10 or WKRG (CBS) because those are the legacy stations that people grew up with. Since the Sinclair LMA they've gone high def, gotten a new set and seen a roster of new up and coming reporters debut. Despite the last place showing, they have really put some emphasis on the news department here. One negative comment is this station has some sound issues that have never been fixed since the big HD rollout. The audio is dull and lacks clarity and sounds like it's being downsampled to 32 kHz, 8-bit. I've sent them comments on it in the past and it was fixed for about three days, then went back to how it is currently. Other than news I never watch so I never followed up. They only run one subchannel here, with 15.2 being a customized version of WeatherNation.
WJTC is this market's lone true independent station (marketed as "UTV 44") with a strong lineup of old and new syndicated programming during prime hours. They have recently begun airing live WPMI news at 6:30pm and 9pm on weekdays.
Overall, my impression is they run the stations as well as whatever network is attached to them. Our NBC and ABC affiliates are treated fairly well with WJTC and WFGX being a tier down but still not terrible. Certainly no worse than WABM or WTTO. WJTC does not run any subchannels at all, and carries all syndicated programming in HD.
There does seem to be some corner cutting evident, though. Like the sound issue at WPMI, and the poor chyron spelling and grammar apparent on their newscasts. And WJTC has been known to have some automation issues on the rare occasion, but other than that, no major problems that I can see.