Thanks for the additional info. Couple of things:
Quote1. Game runs at 800X600 Resized to 1920X1080 unless you run it at fullscreen from settings menu
Why are you using a 4:3 aspect ratio, but then switching it to 16:9? This can lead to all sorts of distortions (haven't been particularly noticeable though). I also don't see the need for having an option to go full screen if the game already resizes to a resolution of 1920x1080.
Quote2. The sprites that are grey get recoloured in game and the Aliens have 3 body parts to make then up!
Having separate body parts was a good design decision. Should allow for more varied enemy types without redoing too much.
Moving onwards, there's two options I see:
1) Continue with your plan to use newly made native sprites drawn 1:1. Be aware though that you'll need to make sure that they're drawn in a manner that is appropriate for the aspect ratio you're using. I'd suggest going with a 16:9 aspect ratio (widescreen) rather than 4:3 (full.screen). 16:9 is equivalent to 1080p which is common among most players according to Steam Hardware surveys. So essentially, you'd create your native sprites to the likeness of a 1920x1080 canvas.
2) Continue with 16:9, but keep a default resolution of 960x540 (windowed mode), and then have the option of going full screen (1920x1080 in most cases). You'd avoid any graphical distortions since you'd only be scaling the resolution by 2x and still maintaining the 16:9 ratio. The (possible, but not really) downside is you'd then create the native sprites to the likeness of a 960x540 canvas, and then scaling them up by a factor of 2. Half the detail than option 1 I suppose, but it really wouldn't be a big deal. Optionally, you could probably just continue using the sprites you have right now (your choice on whether you want to use them or not, but I think they look pretty good).
If you go with option 2, I'd advise against scaling too many sprites up and down, and instead work with a single, consistent native scale for all the sprites. You could have a special category of sprites (HUDs, effects etc.) for which you'd initially make a large version, then scale down to maintain its native resolution. This would allow for a higher quality HUD and more "HD"-looking effect sprites rather than looking blurry or pixelated. I currently do this for my own project and the results are pretty good.
QuoteHumm well the hole game is built around 32X32 Tiles system so here a pic i quickly made after work to help explain
If you go with option 1, you'd probably have to draw everything around maybe a 64x64 tile system or even 128x128, since 32x32 would be too small and possibly cumbersome to deal with. Under option 2, you'd likely keep it 32x32.
Quote3. So a normal sprite should fit in 32X32 a big one will be like 48X48 and a Huge one 64X64 witch wont fix through single 32x32 doors!
I hope there won't only be 32x32 doors. Some outside areas with large hangar-like doors are surely not off the table, are they?
Lastly, if you do go with option 1 (which you've implied), I'd like a sample of a 1:1 sprite before I can contribute anything, just to see what kind of art style you plan to go with and to ensure consistency.