Here are some I've seen:
-Vergil was supose to be captured and turned into Nelo Angelo after their moms death. Yet in DMC3, he grew up on his own and became who he was in DMC3.
This was mainly caused by a change of authors and story telling but I think a game that takes place before DMC3 and is about Vergil can fix this unless if Capcom doesn't mess this up too. Plus its mainly a matter of just fixing the error through logical thinking like that it was Trish who said he lost a mother and brother 20 years ago(that was the only hint) but some can say that it was a rough estimate(calculating both his mom and Vergil) and in the manga Dante thought that his brother was dead til he saw him 1 year before DMC3. I can easily overlook this and as an....umm....necessary plot hole that can be ignored.
-Nero's origin never explained, but it has something to do with Vergil.
I though a plot hole was something that contradicted the plot not an unexplained question that can easily be answered if Capcom has the right writers and has it organized.
-What happen to Dante after DMC2.
Same as the one before it.....not a plot hole and can be answered easily in a sequel to DMC2.
-Why didn't Sparda defeat Mundus ages ago if he was strong enough already.
An army of demons.....I guess an army of demons and even the demon overlord was too much so had to use up his power to just seal them all away and well seal away and bind Mundus and Mundus isn't easy to kill and he is still alive despite getting trashed by Dante twice.
-Dante's bipolar personalities with every game.
This can't be answered that easily or at all.....DMC3-DMC1 makes sense, DMC1-DMC anime makes some sense plus Dante was depressed based on events that precedes DMC1 like Trish leaving him, DMC anime-DMC4.......I guess Dante just has a different outlook returning to his DMC1 self but with more of a DMC3 type attitude or being just an overpowered demon hunter after kicking Mundus's and Cid's ass just gave him a more cocky attitude plus DMC1-DMC4 Dante is a believable change, but DMC4-DMC2 for that to happen it must be a pretty long time-span(I hope not for Nero might be in his late 20's and that won't be much fun) but DMC2 Dante isn't like a soul less ginger plus DMC4 Dante at the beginning(from when he killed the pope up to the end of the battle with Nero) was like his DMC2 self...serious and rather quiet mixed in with some killer intent. His DMC2 even has a kind demeanor like when he gave Lucia incentive to keep living and the coin trick was like him giving Nero his brother's prized sword and even believing in him and letting off in multiple occasions. I guess Dante matured into a serious and fearless devil hunter like his father but still retains his old DMC1 quirks like being very nice and supportive to girls, saying "Devils Never Cry", sure he is rather quiet and doesn't say any witty comebacks but when DMC2 bosses doesn't talk or say anything its hard to say anything smart back. I guess a road trip in hell might alter his personality a bit too.
That's the ones I'd like to get answered.
Now excuse me cause I'm out of here.