Firstly, before everyone jumps on each point and says Im an idiot/mark etc for making certain points, I should make clear that by saying one is better than the other in some respects in no way means the other is shit.
I can see the comparison.... a bit... but I'm not convinced. Although Michaels was a smaller wrestler and yes obviously he had bags of charisma and in-ring talent, theres a lot different between the two. Firstly, Bryan is a master technician and I think his in-ring ability outshines Michaels despite the fact we all know Shawn could put on a show and a half, he was more WWE-mould entertainer/brawler i.e his stand out matches involve twists and turns and gimmicks (i.e ladders) whereas Bryan has put on some of the best 'Pure' wrestling matches in modern history.
In turn of charisma, I think Michaels more organically connected with the crowd and this led to the then-WWF pushing him, whereas Bryan has really had to create a character and earn the right to show his charismatic and entertaining side within that character. This has led to the WWE being less enthusiastic and confident in pushing Bryan, whether it be because hes an indy IWC darling or whatever, but it has meant Bryan has had to work a lot harder to get to even being close to the modern day HBK spot in WWE. Michaels on the other hand was always supported by McMahon as soon as he left the Rockers and adding in his pull with the Kliq means he had a much less challenging rise to the top.
All in all I think they are far too different to really be compared, arguably better comparisons for a modern day HBK would be with Dolph Ziggler (although he hasnt worked his way to the TOP yet), but I've seen plenty of threads on that so lets not open those can of worms again shall we?
P.S sad to see soooo many negative comments already arising about Bryan, before his push there was barely member on these forums who would speak bad of him, now he's suddenly not that great in the ring and only getting over on lame catchphrases that he's 'forcing' the fans to partake in.... oh how fickle some people can be