"Channel 5 used to be a huge #1 in Syracuse. Channel 7 used to be a huge #1 in Buffalo. Both are now owned by the same company and both have dropped to #3 in their markets hmmmmm."
Doesn't have as much to do with changes in ownership as changes in anchor.
Channel 7's appeal in Buffalo was very much tied to Irv Weinstein, and it began to fade after Irv turned 68 and retired back in 1998. (They've talked with him about bringing him back as a commentator to try to pull in viewers again, but AFAIK nothing has come of it so far.) In Syracuse, Channel 5's popularity was a function of the popularity of its longtime principal anchor Ron Curtis. He first of all reduced his airtime during the 1990s because of health issues, then retired in 2000, not long before he passed away. So, sadly, the option of bringing him back in any role is no longer available.
Neither station succeeded in developing and holding on to a successor--although ironically both stations launched the careers of men who would later move across town and take over the #1 position in their market while anchoring at competing stations. Former Channel 7 co-anchor Don Postles, together with Jacquie Walker, now leads Buffalo's news ratings over at Channel 4. And in Syracuse Rod Wood, who started as a weekend anchor at Channel 5, later ran the news shop at sister station WHEN (AM) before jumping to WSYR-TV 9, where he leads the market today as he has done for many years. If 7 had held on to Postles and 5 had held on to Wood, those markets might be very different competitively now than they have been over the last decade.
WHAM-TV doesn't seem to be making the same mistake in Rochester. They've long been grooming Doug Emblidge and Ginny Ryan to be the successor team to Don Alhart, who has dominated the numbers for years. Don will, of course, be on the air as long as he wants--at least until his current contract runs out at the end of this decade. He hasn't lost a step, so there's no reason to believe he won't be around even longer than that. But whenever he does decide to take it easy, 13 is probably far more ready to fill his big shoes than their counterparts in Buffalo and Syracuse were. They have familiar and well liked people in place and prepared to carry on.
I haven't been around Syracuse enough lately to know if WSYR-TV has prepared anyone to take over when Rod Wood (who is now 65) decides to retire. If they haven't, now is the time to start, or else they may tumble just like WTVH.