Yes, of course there are plenty of things that really pissed us fans off, but carefully consider the capacities of shonen manga, and you'll see that OP delivers with exceeding expectations. A lot of the things you guys mentioned had to do with what shonen mangas pretty REQUIREs. Things like staged fights and miraculous (and perhaps inconsistent) recoveries are just part of what all shonen mangas entail.
In fact, I think Oda tries very hard to break these stigmas. For example, I loved the fact that none of the crew had any "power-ups" in the traditional sense until the EL arc. There's also almost NO chapters spent entirely on training (they train, but it's never the topic of a chapter).
One of the greatest things about Oda's writing is that EVERY CHAPTER has something new happen; something introduced; some significant event. I HAAAAAAAATE it when I read a chapter of Naruto, and barely anything happens. The most recent chapter for example (397), the whole chapter is a single conversation, where 1 or 2 things are revealed (Itachi wasn't all bad; he gave sasuke the amaterasu). Or how bout in D gray man and ESPECIALLY Bleach, when the whole chapter is a set up for a cliffhanger; no seriously, the chapter would begin with the hint that "XYZ" is going to happen, and then it's stalled by the charctr's THINKING about "XYZ" and then at the end of the chap, the reader finds out that "XYZ" MIGHT happen in the next chap. I don't know if you guys will know what I'm talking about, but if some idiot Bleach fan wants me to find some examples of poorly written chapters I'll find at least half a dozen.
Seriously, Oda RARELY makes mistakes like these