Long story short: Custom stages brought about no issues when implemented in tournament play. They were easy to set up from an SD card, brought about no crazy changes in results, and were some of the most popular CPs. Some people didn't like them, but they were mostly the same people that say things like "no custom moves" and "Why aren't we playing 2 stock FD only" -- all around worthless people to get commentaries from, because they hate change and everything close to change.
That said, the limitations of the stage builder made it
very difficult to make good stages. There were glitches (olimar's pluck) and huge limitations. Wii U might not have it. Most of the legitimate complaints were due to things we couldn't change due to those limitations. A few hated that we couldn't play on the stages in other tournaments, thus making practicing on them kind of pointless in the long term.
Long story long:
Here's a video on one of them:
http://www.youtube.com/watch?v=J4MtPy6Q0co
I used these stages:
The general results were.... neutral. I used them for an entire circuit (one full season), no major incidents and it wasn't a big pain to implement.
There were no issues with loading them up onto another Wii (we just put them on an SD card and transferred them, with two people it took no time at all).
There were no major balance issues.
Libra and Equity both became very popular stages and helped reach a "middle ground" of sorts.
Equity made the game MUCH faster paced, which was its intention. Libra allowed for an FD that didn't force a player into a chain grab situation all the time. The goals we set for those stages were basically hit, just unintended consequences we couldn't get around were the real drags.
The pros:
-We were able to add stages that increased CP possibilities both for and against characters; MK did very poorly on both Abyss and Libra and Snake did well on them during the time we played.
-It was exciting for players. Those that felt worthless before suddenly felt they had a chance because they had "practiced the stage". A "season" of custom stages was considered as it revitalized tournaments quite a bit.
-It helped meet both sides in the middle. Originalists wanted a broader stagelist, constructionist wanted less janky stages, custom stages allowed the possibility of both.
The cons:
-People who hate change hated it by default
-It was an unknown variable, so when someone had a really good game on a custom stage they ended up being blamed for "abusing" the stage. People blamed losses on them.
-It required initial setup. While minor, it was something a TO needed to do. Just another thing on the list.
-Some disliked the idea of learning new stages that weren't in other regions
I have no idea as to whether or not we'll need or want custom stages for the Wii U version. The 3DS version's stagelist is practically non-existant, even by my standards, but we don't know the impact of that yet. Wii U may have a huge stagelist or an even smaller one, who knows?
Just know that when it comes time to discuss custom stages, previous testing in Brawl found no real advantage or disadvantage to using them that was so overwhelming it demanded their use. If it turns out that every stage for Wii U has a dragon that comes out and slaps the stage and gives speed nerfs and damage buffs to random characters I'd recommend them, but prior to a stage crisis it's kind of a "meh" thing.