I mean... unless the Ent-B is heavily refit, the Red team has a significant advantage in this matchup. Ent-D and Voyager both have more advanced weapons, shields, sensors, and warp than the Ent-B does, and while Defiant is slightly more advanced than the Ent-D, Voyager and it are more or less peers technology wise.
However, Red Team has a significant speed advantage, with the top speed of the Ent-D being Warp 9.8 and Voyager's top speed of Warp 9.975 compared to the top speed of 9.5 for the Defiant and unknown, but still likely lower, of the Ent-B. While that seems insignificant, remember Warp speeds are a logarithmic scale, thus 9.8 is many times faster than 9.5 to say nothing of warp 9.975. Thus on overall technology Red teams gains a point.
That said, tactical ability heavily favors Blue team, and further both Sisko and Kirk have experience fighting opponents that have significant advantages over them and both are much more martially focused captains. On the other hand both Picard and Janeway tended to deal with opponents that were peer to inferior with a few exceptions that aren't really applicable here (the Borg). Further, Picard and Janeway both have serious ego that likely would lead to less than optimal cooperation with each other and personality clashes; whereas Sisko greatly respects* Kirk and has show strong capability to cooperate in tactical situations.
Thus when it comes to tactics, point goes to Blue team. Will it be enough to overcome the tech advantage of Red team? I'm not sure. A real question will be how well they leverage the abilities of their respective crews.
So, when it comes to science and analysis you have Jadzia Dax and Spock going up against Data and Seven of Nine. This is... hard to call. Dax has lifetimes of experience to call on and Spock is a legendary science officer whom everyone else is compared to. Meanwhile Data is a peerless intellect and Seven carries a wealth of knowledge of the Borg with her. Seven arguably has more knowledge than Dax, but because she was merely a drone that knowledge is often fragmentary, whereas Dax's knowledge is truly and hard gained... so while Seven may have more, she has a harder time leveraging it to be useful whereas Dax knows well how to apply what she knows. To be honest, given things here, I don't think either team has a strong advantage... so a tie in this category.
Tactical officers becomes the next question. Need to be able to hit with those weapons. On Blue Team we have Chekov and Worf going up against Red Team's Tuvok and... Worf. Chekov never was stated to be some brilliant officer in this category, but by showing in the space battles he was in he was level headed and generally highly accurate, even managing to hit targets well with minimal assistance from sensors (Battle of the Mutara Nebula). Meanwhile Defiant Worf has considerable experience and is on a ship that highly suits his combat style. His track record on Defiant seems to be better than on Enterprise-D, but in general, he's the same person with the same capabilities. Finally Tuvok has considerable experience with a starfleet career that included service on the USS Excelsior itself, and while the Ent-B is a refit, it's bones are still an Excelsior-class. Further through all the engagements Voyager found itself in he showed consistent ability to hit targets and maintain a level head. So with one identical character on both sides, the real question of advantage comes down to Tuvok vs Chekov, and for all I love the good ol' Russian, I think Tuvok showed greater ability as a tactical officer, plus brings extra knowledge of an opponent's ship. Point to Red team.
Now we get to how well will the ships be piloted. Helmsmen of the respective ships were generally Sulu for Ent-B, Jadzia for Defiant, Tom Paris for Voyager, and Random Extra #552 for Enterprise-D (no, seriously, there was no formal "helmsman" character for TNG... sometimes it was an extra, sometimes they had Worf or Data or Wesley handle maneuvers). As good as Tom Paris is, and he's by far the best SINGLE helmsman here, he's only the helmsman of one ship. Meanwhile both Jadzia and Sulu are highly competent helmsmen with long experience and respected in their craft. Paris can't really make up for the fact that an extra is piloting the Ent-D and as such the edge here likely goes to the Blue Team.
Engineering will be critical for damage control and getting every last miocum of ability from their ships. In this case, well... it's honestly no contest. In the Blue corner you have the literal engineering legend of Montgomery Scott, the literal Miracle Worker himself teamed up with Miles O'Brian, one of the single most brilliant and adaptable engineers Starfleet ever produced. LaForge and Torres are both highly competent, adaptable, and skilled, but they're not Scott and O'Brian. Those two managed their ships in some of the worst situations and they've held through it all. Point to Blue Team.
Medical personnel I'm not sure how critical they'll be, but to rate them you have McCoy and Bashir against Crusher and The EMH. This is... again REALLY HARD. All these doctors have some brilliant accomplishments to their names and have pulled out medical miracles to save more lives than any other four doctors in Star Trek. I think... I'd have to call tie on these ones too.
So going by points you have Red 2 - Blue 3, but one of the points Red has: Technology is a major advantage.
So I'd guess that in scenario 1, no prep, that tech edge is going to be the deciding factor, and likely goes to Red Team. The firepower differential is just to great between an Intrepid + Galaxy vs a Defiant + Excelsior-Refit. Clever tactics and general analysis won't be enough to overcome those advantages.
However, I think scenarios 2 and 3 go to Blue Team. Once you give them time to prep and adapt, O'brian and Scotty will figure out ways to bridge or nullify the tech gap, and Kirk and Sisko, along with their core teams will figure out creative strategies to use against Picard and Janeway. Meanwhile Picard and Janeway both tend towards arrogance and strictly by the book thinking, this tendency will make them more predictable and further they'll get into an argument of "who's in charge", with both holding they should be the one in overall command (meanwhile, Sisko and Kirk will have a quick talk about it and decide which one of them is in charge, and that will be that). Overall what this means is that the more prep time they have, the more likely it is that Sisko and Kirk wins, and the less cohesive Janeway and Picard become.
-------------
* "Fanboys" might be a more accurate term for his attitude towards Kirk as seen in "Trials and Tribbleations".
