I also think its a manner of a personal preferences , some people prefer Vanilla\Stock over Manufacturers UI
Personally , I find the vanilla is very boring (yes you can customize it as you want , but still , plus I hate it) & I prefer Custom UI instead (Motorola's new UI or Sense)
Some People prefer vanilla because its lighter on the device & doesn't run every single app in the background (this is not the case with me) , unlike Motoblur & Sense phones
But Manufacturers UIs also have their advantages over the vanilla , especially in the Media section (better Camera app , HD recording , Better Music player ..etc)
Here is the catch though , having a Vanilla UI outta the box doesn't guarantee that you will have the latest updates faster , I'll give you some examples :
1 - Im speaking of a personal experience here :
I've an OG Motorola MILESTONE (the GSM variant of the OG DROID) , the MILESTONE was the first ever to receive Eclair 2.1 (the phone actually came with 2.0) , even before the OG DROID (& probably the Nexus One) , but I got the Fro-Yo 2.2.1 update about 4 months ago (as soon as it was released for IEME area)
2 - The British Nexus One received the Official GingerBread about month & a Half ago , after the DROID X & Desire HD got it
3 - the LG G2X (vanilla Froyo 2.2.1) was released about the same time as the ATRIX 4G (MotoBlur on top of Froyo 2.2.1) , but the ATRIX got GingerBread 2.3.4 first (The Atrix 4G is the first Non-Nexus device to get 2.3.4)
As you can see , it depends on the Manufacturer & the Carrier to release the update & when it comes to Europe & the Rest of the world , is a whole anther miss Since Manufacturers have to get Carriers approval & the "Communications ministry"'s approval in every single country , then carriers start testing it for couple of months , trust me been there before
After all , you will pick whatever you like the most depending on the Spec.s that suits your needs & desires