3 will always be my favourite, even as flawed as it can be.
1 is too janky and hard to play at times and 2 - while a great game - ultimately feels like a 30 hour filler episode to me while 1 and 3 are either side of it working the Reaper plot.
History will favour ME3 greatly as time erases the original ending controversy.
I agree with you regarding 2 especially once you start playing 3. As someone who played them for the first time recently, I thought the main story of 2 was just boring and the Suicide Mission did not meet expectations after all the talk I heard of it over the years. Although Kasumis' DLC and the Shadow Broker DLC in 2 were easily my favorite parts of the series and are possibly my favorite DLC to date.