Yes, I'd remake all of it, actually. Either make it a prequel or make it more based on the true story after Balto saved Nome.
But considering its still the same movie, just a few changes, then this is what I'd do (i dunno if its what the topic asks, or not, but oh well).
1) Give the plot an extra 10 minutes of thought.
--An extra 10 minutes of thought is just enough time for me to figure out that the movie sucked with all of 99.9% of the magic. It would let me (and my crew) think of something like this: Jenna and Balto have puppies, with a less lame introduction (cuz face it, things like "They're so beautiful...just like you." are cheese-tastic) I would love to go into detail in this, but this is already gonna be a long post.
2) Change everything about Aleu: change her voice, her personality, and her looks. (Reasons why located here at my first post:
viewtopic.php?f=2&t=7214&st=0&sk=t&sd=a&start=30)
3) Give Jenna more screentime, action, and a less-lame personality. I know her personality wasn't the most elaborate in the first movie, but the sequel is a perfect chance to fix any "mistakes" in the first movie.
4) Make Muk and Luk less retarded and give them an actual purpose in the movie, like in the first movie. Like, without them in the first movie, Balto would've drown.
5) Exclude most, if not all, magic.
6) Give interesting characters like the vixen more screentime.
7) Make Niju more wolf-like and give him a more in-depth character. Like what did he have against Nava? Why was he afraid of change? Why was he the worst antagonist on the face of the earth?

Get rid of Nuk, Yak, and Sumac. Just because its a Balto movie, doesn't mean it has to have a "trio" to save its comic relief.
9) Make Nava less loony.
10) Explain why Aniu was so "great" cuz they pretty much leave people thinking "What's so great about Aniu anyway?" She doesn't even have 30 seconds of screentime. I'd also make her not white (I'd make her glowy, see-through, something not-white). Cuz anyone who knows what an Arctic wolf looks like sees nothing special in a white wolf. Besides, if you're bored out of your mind and think deeply into the fiasco that is Wolf Quest today, you will find the white wolf thing a little racist. I would also not make her Balto's mother (religiously, maybe, but since animals are not known to have any kind of "religion" that won't be included. Besides, people throw fits when movies have something religious in it, anyway, especially if its incorrect)
11) I'd make Balto explain his past a little more clearly. Like a flashback. Know what those are? Those are nice.
12) I'd put the characters in very dangerous danger and not make it a huge joke. Who is Balto and Aleu to crack not-funny comments while their life is on the line fighting a huge rabid bear? They're not imortal and they sure as heck ain't experts in any type of combat (Because face it, Balto is not a fighter, otherwise he would've did some biting and fighting and OWNING in the first movie) And in turn, I'd have some character deaths. Maybe I'd actually kill off Nava and Niju. Maybe Aleu does get crushed by the impact of the iceburgs. Who knows? It'd be dramatic, and sad.
13) I wouldn't change the backgrounds too much (maybe have Grah do them >D) but the animation, for SURE. I know a buttload of people who can animate ten times better than anyone who animated B2.
14) I wouldn't have Aleu become the leader of the pack, unless she was at least 4 years of age. A one year old leader doesn't contribute anything to my happy side. It just screams "Yeah, we're like Weed." Sure, I'd make her and any other sibling I decide to throw in there become a MEMBER of the pack, but not the leader. I'd just throw in a new character who would become the leader (and probably giving Aleu or whoever a love interest in the process) or just keep Nava as the leader or something, I dunno. Anything's better than making a one year old pup a leader of an entire wolf pack when it decides the fate of it.
There's more to mention, but if I feel like editing it later, I will.