Ok, so I'll try to raise the ceiling on tight areas. Will that help?
Make more rooms? So that they can hide and flank? Or basically just make something to hide on like big props?
Generaly the flank and main path are both in the same room/area. Look specificly at mannhattan and rottenburg on where they put the raised sections, and side paths. A flank doesnt always mean a completely alternative path.
To allow such raised area that can feature as a flank, the room generaly needs to be larger in width and height and often contains some cover aswel. In most mvm maps the roof is about 1024 HU above the players and only small sections go below that. Which is why you rarely see narrow indoor sections (but still, all valve maps do have these sections, but only short ones). The roof can provide a hinder, but at the same time also add variation.
This is realy the part that takes most time in mvm making. The area itself must play ideal before missions even come into play.
So... put random displacements like the dirt in mvm_mannhattan?
Its not always displacements. Sure, they are the easiest to perform. But if you look at mannhattan spawn, you notice the first drop exit is 128 units lower and doesnt smoothly align to the ideal sniper spots. Same for rottenburg and mannworks. Older maps actualy do have this smooth view, but at the same time its hindered due to being at ground level.
For indoor sections small piles of rubble, some gap in the floor etc can give just enough variation. There is no need to make the entire floor a displacement. As long as key sections are taken care of. The closer to a sniper, the higher the risk anyway. and here comes the point where the risk becomes too high, this is why rottenburg is one of the harder maps to snipe on yet coaltown and decoy are easy (since they have relatively safe spots for a sniper with a quite flat ground for bots to walk on).
Displacements have a 2nd effect: a better nav. More smaller squares works better than just a few large ones. The AI can sometimes act dumb. Flat grounds have 1 advantage: splash damage doesnt go through the shield and can in some cases make a sniper area which is considered risky a better option.
There is many factors and usualy it requires playtesting. but its a must to think about it, you cant decide these things in late beta anymore. Its often too late. Mannhattan already has such bump of rubble between 1st and 2nd capture which was clearly ment to block sniper vision.
Its always good to look at existing mvm maps and try to figure out the fun parts, and why they are fun. At the same time, if you know flaws in those maps. you can check for those in your own.