It's not any one thing in particular that gave Vista a bad rep. It's a combination of things creating domino effects...
Generally, some of the issues were:
1) Its original code base, which got scrapped and rewritten with Server 2003 as its basis after the whole Blaster worm fiasco, which lead to:
2) Its development delays, partially due to having to work on XP SP2 post haste, which lead to:
3) Promised features being omitted (i.e.: Indigo, Avalon, etc.)
4) Developers dragging their feet on Vista-compatible drivers and software (particularly because many of them followed standards that should have never been followed in the first place like having their stuff work only when running the machine as an administrator).
5) The whole "Vista Capable" fiasco orchestrated between Microsoft and Intel. Particularly, many of Intel's onboard graphics adapters didn't support Aero at the time.
6) In general, average PC hardware not ready for Vista at the time. This was before 2 GB of RAM became super-cheap. There were Vista Home Basic machines running 512 MB of RAM (my cousin had one), which completely drag their rears trying to anything. This lead to...
7) "Why pay more for less? XP runs just fine on my current hardware!" XP was not only the official successor to 2000, but was the unofficial successor to Windows 98 and Me. XP is an NT-based OS for both consumers and businesses. Despite any negativity toward XP back then, it had a lot of obvious benefits to consumers. Businesses, OTOH, were not so quick to go to XP from 2000, as they had the same complaint mentioned below that applies to Vista:
Vista Gold/SP0/RTM's bloat. Considering that Windows 7 can run on a netbook and Vista struggles in that department, it seems that there wasn't much in the way of code optimization in Vista. Perhaps the 11th hour rush post-code scrap had something to do with that? Perhaps Microsoft thought that people would throw hardware at the problem instead of sticking with XP?
I used to tell people not to run Vista on anything less than 2 GB of RAM. Granted SP2 can run on 1 GB of RAM passably, it shouldn't have taken that long to clean up the bloat.
Remember slow file copying in Vista? That wasn't fixed until SP1.
9) Too much change too fast (i.e.: User Account Control). People hate change for the most part. People despise change "just for the sake of change." That's what Vista presented itself as. Was Vista fulfilling a perceived need that XP was not? In general, it did (widespread 64-bit adoption, better security model), but people didn't see it that way.
10) Removal of previous features with a) little justification for doing so and b) no solid replacement (i.e.: NetMeeting, HyperTerminal, NTBACKUP, etc.). NetMeeting was replaced with Windows Meeting Space, but the option to enable Remote Desktop Sharing to allow the person on the other end to see what the remote controller is doing was removed. HyperTerminal was removed with no replacement. NTBACKUP was replaced with the Windows Backup in Vista, which is not as flexible...
11) Far more rapid spread of information in the late 00s than the early 00s. Naysayers are louder than ever, and they're being heard whether they should be or not. This leads to:
12) Misunderstanding of Vista features. Superfetch is probably the biggest example of this. Some say it slows down computers with less RAM. Some say it slows down computers in general. This may be because we're all trained to think that seeing all our RAM gobbled up is abnormal when, in reality, it's actually caching files that it thinks we access the most so they can be accessed faster. However, one thing I've noticed is that it does slow down startup/logon during the caching (which is why Windows 7 delays the caching by about 5-6 minutes). Perhaps this is why Microsoft defaulted the Start Menu power button to "Sleep"?