I agree. I've noticed that if you sync regularly then it's pretty fast, implying the longer between updates the more pain you're buying yourself.
However, it does seem like something that could simply 'trickle' in the background - perhaps with a system setting that if you're online the system should sync whenever it can without impacting foreground applications.
I think it's just an example of where the designers where thinking a certain way - in this case store Trophy's locally, then sync only when the user either accesses his Trophy's or his Gamer Card (which are the two triggers I know of) - rather than perhaps taking a different angle from the start, such as how do we make this automatic and transparent to the user.
TBH, although I prefer the XMB approach to 360 dash, I think the 360 OS is better thought out in terms of installs, downloads, etc. with PS3 leaning towards multiple step, user initiated processes such as download then tell me you want to install.
Another approach would be to simply have it sync if the PS3 is powered on, online and not being used. Again this could be a system setting.
Off topic - I'd note that no minor irritant like this comes close for me to the almost Universal 'press button X' to go to the main menu to actually then start or load games. That drives me mad (and the fact it seems to be transferring from consoles to PC versions of games (such as Mass Effect) is only making me madder). WTF do they do that? It's totally against 101 ease of use!
Anyway, short term, the best advice I can give is use your PS3 more and sync more regularly, that way each sync should be shorter! You'll no doubt be loved and adored by the heavy duty PS3 fans on the site.
I'm not too bothered by Trophies myself, but I just got into the habit of checking them at the end of each game session to have short sync times - I go grab a coke or a beer or something and by the time I'm back the sync is done and a I power down.