I figured out the culprit for the planets markers in the Galaxy Map, it's HUD Scaling in Flawless Widscreen (FWS). When I disable it and then engage the Galaxy Map it works but everything else is borked like the planet descriptions, menu and etc. It seems the fix with FWS isn't identifying the changes. In ME1 I just disabled FWS all together with a hotkey and I could navigate the Galaxy Map just fine but this having to alt+tab constantly is annoying. I am running the Origin ver since I didn't have to manually install the DLC one by one, also bonus info if got the base game of ME2 on Origin (it was On The House at one point and glad I grabbed it now) it will recognize your DLC and will download it into your game even if you owned it on Steam first, which was my scenario. This version is not detectable by Widescreen Fixer (WSF) even though it is running, says it does support Origin and yes I am running English and not another language. I have no idea what's up but I can't figure out how to test this any further with WSF. Hopefully this helps someone.
EDIT: Okay I figured out a dirty trick to make this work faster since I run secondary monitors. I went into my GamerSettings.ini ( in ... Documents\BioWare\Mass Effect 2\BIOGame\Config) and changed Fullscreen=True to Fullscreen=False and I also changed BorderlessWindow=False to BorderlessWindow=True. This lets me quickly alt+tab in and out of the game without having to minimize and reload shaders when it was fullscreen. I wish there was something more permanent I could do but this is all that works and you can't hotkey specific features in FWS, only whether or not if the fix is enabled in general.
Edit 2: I just figured out something else that makes it easier to navigate the Galaxy Map. Do what I mentioned before, disable HUD Scaling only and then bring up the galaxy map in game, after it is up everything will look smashed together but at least the markers will be over the systems and planets. Than you need to disable the fix completely, the default hotkey for this is ctrl+alt+z. This will stretch the galaxy map so it isn't all smashed together. This makes navigating way easier but since it is stretched you do have look around a lot more. The UI will be borked when you go to a planet or refuel ship in system so you will have to reenable the fix and hud scaling but, if you need to go to the galaxy overview for choosing what system to go to, just double click on the mass relay, in the glowing part works best. If I find any other tricks for this game I'll let yall know.
With Fix and HUD Scaling enabled
With Fix enabled and HUD Scaling disabled
With Fix and HUD Scaling disabled
Edit 3: And if you need fuel with the HUD Scaling disabled you can just double click on the fuel ship and you will get fuel, for probes you'll need to reenable the the HUD Scaling to get the prompt to buy probes. To make things a little less confusing here is what I do to make this complicated process work.
Navigating the Galaxy Overview Map:In game at Normandy's Ship Holo and Galaxy Map > Alt+Tab out of game to FWS and uncheck HUD Scaling > Go back into the game and engage the Galaxy Map > Disable the fix either by hotkey Ctrl+Alt+Z or Alt+Tab out again and uncheck it than go back into the game > Head to a Mass Relay and double click on the blue spinning animation > The Galaxy Overview of systems should look like the third picture above.
What you will need to do in a local system is:In game at Normandy's Ship Holo and Galaxy Map > Alt+Tab out of game to FWS and uncheck HUD Scaling > Go back into the game and engage the Galaxy Map > The Hud will look fine with the names and mission descriptions.
When you're in a system I don't recommend disabling the fix because the text isn't as cluttered in local system as they are in the galaxy overview.
What you need to do to interact with planets with the resource minigame, land on planets and buy probes:As I mentioned before you can double click on a refuel ship to get fuel and a mass relay in the blue spinning but also double clicking on a planet or system that the Normandy is sitting on will bring up the next menu but it will be unusable due to HUD Scaling being disabled for a planet. HUD Scaling cannot just be enabled and it work like the disabling and reenabling the overall fix, you
MUST go back to the Normandy > Alt+Tab out of game to FWS and check HUD Scaling > Go back into the game and engage the Galaxy Map > The Hud will look fine for the planet and refinery ship if you want to buy probes. This also must be enabled to to scan for resources.
This is a pain for sure but it's the only thing you can do aside from dropping your resolution to 1080p.