There is some overlap between TNG and DS9 (and DS9 and Voyager as well), but I'm not sure it's worth the trouble to watch all the multi-show episodes in strict "order"...and one would also have to work in the feature films to do that. Think of them as books in, say, a trilogy...books that tell different stories that happen to overlap in a few places but works well enough as a whole without the reader needing to skip around.
Yes, Season 2 of TNG had a lot of problems (writers' strike, chaos on the set, etc.) but it had several episodes that shouldn't be missed, and is still better than most TV shows as a whole. Don't even think about avoiding it