Pros:
I agree with pretty much all the Pros mentioned by Kuudere. I picked up my pre-reg badge first thing Friday, and it was smooth as butter. I will say though that I can see how it could get confusing during busy times with about six computers per one printer and one person to collect the badges from the printer. Maybe it would help if they would prompt each table to form a line to pick up the badges after you print them?
I'll second the recommendation to bring Adobe back next year and I'd even go so far as to suggest making it a permanent partnership. This is exactly what Fanime needed to take it to the next level, in my opinion: a partnership with a relevant professional company, in this case a tech company that makes software useful for people who like anime (and bonus points for being local!)
I loved the setup of the convention center, with a badge check required before going up to the second floor. I don't think ghosting is good for the con, so I'm all for cutting it out. The signage was also very clear and sharp looking. It didn't look like badges were checked when going into the area where the viewing rooms were (or the viewing rooms themselves)...were those officially free?
As always, MusicFest was top notch. I was a little hesitant when a US band was announced as the opener even though they are on a Japanese label, but Phoenix Ash turned out to be very good, and I would gladly see them again. After all it is better to have two bands than one. And of course X4 was amazing.
The panels I saw were great. Glad to see the Awesomely Bad J-Music Videos panel back, and on a whim I went to the Anime to See Before You Die (18+) panel which was also very very good. I liked his presentation. Also at the guest panels, Moderators did a good job blocking ridiculous questions/requests.
I am VERY glad that Clockwork Alchemy is being spun off to a separate location & weekend next year. I feel like attaching it to Fanime has done both conventions a disservice.
Overall, Fanime felt more professional than ever before. Previous years in my view it has always been kind of a mess even though some years it was a better organized mess than others. But the convention really put on its big boy pants this year. Social Media presence and tone was vastly improved. As mentioned before the Adobe partnership was brilliant, and it was nice to see a big presence from Crunchyroll and Viz, Bluefin Tamashii in the Dealers Hall, and official panels for Sailor Moon and Mobile Suit Gundam Thunderbolt: December Sky. (I wish MSGT:DS wasn't at the same time as MusicFest and would have loved there to be an additional screening...but at least it was nice to have options!)
Cons:
The Artists Alley was great, but agreed that the first three rows were a fire hazard.
I got up early on Sunday to see Ultraman X in the Asian Film Room, and it turned out not to be the film, but episodes 1-5 of the TV show.

I still like the TV show, but if something is in the Film Room I expect it to be a film unless otherwise specified. On the description, all they would have had to do is write "Ultraman X: Episodes 1-5" or "Ultraman X: TV Show," etc. (Similarly, I expect everything in the Marathon room to be TV episodes unless noted. The Nostalgia room could go either way.)
This next one isn't Fanime's fault at all, but I was disappointed at the lack of Gloomy Bears in the dealer's hall. Every year I've been able to get at least a couple interesting ones. This year, as every year, I scoured the entire hall...but only found a grand total of two, both of which were fairly generic/bland designs.
But none of my complaints are too major. This was my favorite Fanime to date, and I really hope that this year is an indicator of how Fanime is moving forward.