Shawn/Jericho isn't in the same league. It's a classic by PG WWE standards, but it doesn't hold up to the classics of the 80's and 90's.
2003 wasn't the same PG programming as we know it today. HBK/Jericho at WM19 was a great match and a classic no matter what way you want to look at it. If it weren't so great then no one would be comparing it to a late 90's classic in the first place.
Both matches were fantastic, but they were from completely different eras in wrestling. One was WWF, one was WWE - different letter, HUGELY significant contrasts in programming. If you compare Bret/HBK to the other classics of the post-attitude era, and then you have to compare HBK/Y2J to the other classics of their own era. To deem a classic against other classics, you have to look at how significant each match was in their own era, how significant each match is of all time, and then compare both.
Whilst I think that HBK/Y2J was a better wrestling match, I think that it is without a doubt that Bret/Michaels will ALWAYS be the more significant match in not only WWE/F history, but WRESTLING history. Also, Bret/HBK was during an era where wrestling was on the brink of an innovative era, so for it's time HBK/Bret was revolutionary, and showcased the kind of wrestling that inspired the likes of Jericho and others to keep up and raise the bar.
If it weren't for Michaels/Hart, then Y2J/HBK would never have been so excellent, and the wrestling we see today may not have been so innovative. Plus, it was matches like HBK/Hart that inspired guys like Jericho to do the kind of showmanship that they did, so you never know, we might of never seen Jericho reach the heights that he did, had of Michaels and Hart never had their epic rivalry.
You can't really accurately compare matches from different eras though. Showmanship is constantly shifting, so what may have been considered a great match 20 years ago may be considered to be boring today. People always dis Hogan for not being a great wrestler, but when he was in his prime, the art of performing wasn't as innovative as it is today. It's like comparing Citizen Kane to the Lord of the Rings. Both are great movies when compared to the standards and innovations of their respective eras, but you can't ever truly compare them.