A 3x3 shower is too big. Definitely less intimate. I like the second plan! What did you decide to do?

Personally, it's better to have a wall between the bathroom and the toilet so no one gets walked in on. Definitely a good idea to keep the bath in case of reselling, although are you planning on going anywhere? If not, get rid of the bath and get a bigger shower I think.

We have a 900x900 shower and it's plenty big enough. Neither of your proposed layouts looks that great, to be perfectly honest, sorry! In the first layout, you could improve it quite a lot by swapping the toilet and vanity (centre the toilet under the window on the bottom right of the picture if possible), and having the shower door on the other wall (beside the door). Then, you could have a towel rail on the wall beside the door (i.e. behind the door when it's open), which would be accessible from the shower but hidden when the door was open. An 800x1200 shower might be a good size for your space. You'd have to choose a toilet that doesn't protrude too far, plus a narrow vanity. With that layout, you could have a long but narrow wall-hung vanity, with a big mirror covering the wall between the windows, which would make the room feel bigger and would give a good amount of storage. Also, you may find this helpful: http://www.houseplanshelper.com/small-bathroom-floor-plans.html?utm_content=buffer4aa20&utm_medium=social&utm_source=facebook.com&utm_campaign=buffer

If you can narrow the linen cupboard, then you do do a similar layout to that GB has shown but with a changed door swing, swap the basin and WC, putting the WC on the wall beside the door so the WC is concealed behind the door.