Two months ago both teams were playing different styles of football which was not like their reputations but now Manchester United have picked up points and are improving whereas Atletico have improved marginally. You are right though, the match will be close and it is a European clash at the knockout stage so anything could happen.
I would find it hard to believe Manchester United would lose the return game at Old Trafford, at worst for them it will be a draw therefore what happens in Madrid will be the important indicator for both teams. If Atletico lose the first game they will probably not qualify but if they draw or win in Spain then what an atmosphere it will be in Manchester.
Atletico fans deserve to see a Premier League team at their stadium in the knockout stage, their fans are brilliant and their new stadium is great. I hope it will be a good match.
I would lean towards 75/25% in favour of Manchester United.
I think Atletico will play well enough to trouble Manchester United over the course of two games (home and away) I think Manchester United will qualify for the next round. Atletico is not playing as it did a couple of seasons ago, neither is Manchester United but if a squad could be said to be bigger with better players it would be Manchester United.
I would not give such a significant advantage to Manchester United in this confrontation. Two months ago I would have given the advantage to Atletico Madrid in general, but the latest results no longer give confidence in this and I also tend to believe that Manchester United have more chances to go further. However, it is worth bearing in mind that it seems that Atletico Madrid made the right conclusions after the defeat by Levante and won a major away victory over Osasuna. Also, do not forget that the first match will be held in Madrid and this is also a factor in favor of Atletico at least in the first match of the confrontation with Manchester United.