Mass-effect – Are there other character-specific sidequests except the ones of Garrus and Wrex

You miss out on a few things, I'd only consider the interactions with Wrex as major:

1. BDTS DLC for the first one allows you to have some war assets if you took the paragon path.
2. Conrad Verner needs to have survived in both the first and second to show up as a war asset in the third.
3. You have to have saved the Rachni queen in the first to gain her as an asset in the third. (The fake rachni queen that's subsituted will betray you).
4. You will miss out on Wrex in general as he's now dead.

There are more but most of them are simply war assets etc.

There are some POIs that do not appear on the global survey map (the full screen map). However, they will show in the mini-map in your display as you are driving around and get near them.

There are no POIs that are completely marker-less and required manual terrain survey—as in walking around hoping that a use prompt comes up. They will always at least show on the mini-map when you get close enough for them to be within the mini-map range. In other words, they will always show in the mini-map.

Primarily these are optional resources that are credits or just more resources. Sometimes the "military tags", "research", etc. that are for completing achievements. None are required or are super special really.