And this sums up the major problems most people have with Shippuden. The Deus ex Machina Kishimoto introduced at the drop of a hat, just to avoid dealing with major issues caused by the characters' actions. Take the Pain invasion you mentioned. Pain destroyed Konoha and killed thousands. It would've been so interesting if Kishimoto sought to explore the ramifications of the deaths. But no. He used a total Deus ex Machina to resolve that issue.

And then there's the ending too. Why bother to pair up everyone? And some pairings don't even make sense. Sasuke and Sakura. Karui and Choji. What? The ending was very unsatisfactory. It just felt like a cheap, naive cop out because Kishimoto ran out of steam.

 

I'm with Sou on this one. Pre-timeskip was decent on the whole, with a handful of missteps and a few truly outstanding moments, and everything post-Invasion is completely bonkers, in a terrible way, but nearly everything in between is great. The pacing is nice and tight, the antagonists are well fleshed out and clearly had a lot of thought put into them, the fights are fantastic, and things are just generally quite well done.

My only significant gripe with that portion of Naruto is the kage bunshin ex machina Kishimoto pulled out of his ass because he can't timeskip properly. It was a worthless ass pull that never should have been necessary. In pretty much every other aspect, however, it's great.

 

Part of the problem with the pairings is that there was a large timeskip. We didn't get to see the characters develop so many of the pairings seem so wtf.
Except for Shikamaru and Temari. Ship it all the way.

 

Personally, the best fight of the series was the Sasuke versus Itachi fight. It exemplified tactics, high end techniques, and all of the shinobi disciplines.

Once you get beyond that fight, its like all of the fights were about who has the higher power level and hax.