Lucario's we are aware of, and we weren't able to fix it. The problem is that when these characters get grab released, the variables that store their ability to use their up specials aren't getting cleared which means they still can't up special. This is a general bug that affects Pit, Lucario, Mr. Game & Watch, Snake, and Sonic. We fixed this by putting a variable clear function in their ground and air breaks which is a per-character change. We found that most of these characters used LA-Bit[61] (Pit, Snake, Sonic) and that Mr. Game & Watch uses LA-Bit[62]. We just couldn't find what variable Lucario uses, and it wasn't for lack of searching. We tested not only LA-Bit[61] and LA-Bit[62] but also several nearby variables, and we even tried asking the people exploring PSA at the time if they knew what variable controlled this. The only answer we were able to get was someone being pretty sure it was LA-Bit[61] or LA-Bit[62] which we of course know is false. If we grinded at it hard enough, we could probably solve this, but frankly, this bug is unimportant enough that we decided to make other things a development priority (the general bug is really only a problem for Snake and is a bigger problem for G&W and Sonic than Lucario). If you know what variable controls Lucario's ability to do up special, please let us know and we will doubtless make use of that.
As per the foostool behavior, I'm not sure that's a problem though it is something to think about. On one hand, I have a feeling that the only one of those five characters who gets his up special back from being footstooled is G&W (who by design gets his up special back under more circumstances than the others), but on the other hand, I can see an argument that it's really weird that Pit and Lucario can get their up speicals back if they are footstooled out of helpless but not out of their falling when they correctly use their up specials to avoid helpless. I'll look into exactly how this works across all five characters, talk with Thinkaman about it, and reach some conclusion.
There are, of course, other priorities in terms of minor bug-fixes. Here's a good example of a bug we currently don't have fixed but would like to fix and is more important than Lucario up special issues:
http://www.youtube.com/watch?v=WWZ_IStFrPc
As per freezing when playing Balanced Brawl, as others have said, this should not happen and does not happen with most people. Your response to the question about custom stages indicates a misunderstanding though. BBrawl doesn't come with unique stages (we're of the position that Brawl's default stages are just plain better than any of the hacked "new" stages to the point that the "new" stages just aren't worth using at all). It comes with a "custom stage" as in a file that is a file read by Brawl's stage builder. This is smash stack. If used in an inappropriately configured code set, it can cause freezing. BBrawl by default is correctly configured. If you monkey with it and remove, say, the "no custom stages" code, then it will cease being correctly configured (that will cause consistent freezing though). If you are a HBC user or the type of user who would use BBrawl with non-default files, we assumed you were an advanced user who would be familiar with this and easily able to edit it to your liking (and, of course, we have no problem with people doing this). Time has proven this a poor assumption, but I can assure you that if you tinkered with BBrawl and are now getting freezing, the most likely cause by far is that your changes are what are causing freezing in some way. I confess that we're doing less troubleshooting these days than we used to, but looking at the differences between how we suggest running BBrawl on our site and how you are running it would probably help you find the root cause of your freezing.
One thing that smash stack will cause freezing with is the "Random" stage selection setting. No, I do not mean picking random on the stage select screen. I mean going into the menu and changing the option for how stages are picked from the default (which lets anyone pick a stage and might also be configured to "winner picks" or "loser picks") to "Random" which in normal play causes the stage select screen to never load and instead automatically picks a random stage. I doubt this is the issue in this case, but if you are messing with that setting after playing BBrawl for a while, that would explain your crashing issues.