Well, we think that he did well considering the data we have, namely
this exit poll collection from right around the ballot time period. I think at the very least we can set a reasonable assumption to being top 10 even if he's not necessarily #2 like in that collection of data. He is a consistently popular character, however; and was bolstered by the help of not actually being in Sm4sh. People assumed the ballot was used as DLC, so that's why Ridley is further back.
Even if people knew that it would be used for further smash games, I think Isaac would still have done strongly. He's typically top 5 and doesn't float too far back from that position. This especially being the case when you can only have one vote to cast.
Why he didn't have a mii costume is down to pure speculation as we never really get much info to work with. Sakurai did talk about the K. Rool costume being there because he was popular I think, but others don't really get that. Not all the costumes were necessarily from the makeup of strong ballot winners. You can go over the list yourself and see it's sometimes comprised of fun little costumes from characters who wouldn't otherwise get in. You have two Virtua Fighter costumes, a Tekken character, two different Monster Hunter outfits, Gil from Tower of Druaga and then a slew of other wacky outfits like a Chocobo.
Dark Samus, Daisy, Simon, Richter and Ridley all had no costumes either yet they're playable now so it's certainly not a hard rule. A lot of the mii costumes feel like a mixture between dream characters, popular ones and seemingly arbitrary ones depending on the whim of the devs. It's nice to use the inverse of the rule to test it really. Does the fact that Isaac not having a mii mean he's definitely not going to be playable? I'd counter with, does Akira from Virtua Fighter having a mii costume definitely mean he's going to be playable? Maybe it would be more illuminating if the mii costumes really was filled with speculated characters. If all of those characters I listed above were alongside Bandana Waddle Dee and every character thread out there right now with a costume with the exception of Isaac, it would be worth looking into. I just can't help but feel that it's a self-imposed rule that just has no true bearing on anything.