I hope you enjoy your first home; it sounds like a great use of your space.
If the finish is much better than the rest of the home, then I hear "I wish the rest of the home looked like the basement" and if the finish is not as good, then I hear "I will have to tear out the basement and redo it" - certainly both are generalizations and there are always exceptions.
If permits have not been pulled, then you may want to explore what can be done now - although there will be some Buyers who will care less as long as the work was completed professionally, there will be some Buyers who will eliminate your home as a possibility if the permits have not been pulled.
Basement finish in your situation will almost double the "finished square feet" in the home and if I was marketing the home, that is one of the factors I would emphasize even if the local MLS does not include basement square footage in the "square feet" field. An additional bath is always helpful so I would think that will help the value of the home.
My experience is that if you have pay a professional to do the work, a basement finish may not increase the value dollar for dollar, but it will help it sell much faster and as long as you are living in it, you will enjoy having the additional finished area and that provides value to you. If you do most of the work, and it looks like a professional did it, then in my area, the value would increase more than the cost of the materials.
The ceiling height issue is probably a function of your immediate neighborhood - if the homes around you also have low ceilings in the basement, then it is probably no issue - if the other homes have standard height ceilings and you have a lower ceiling, then Buyers in your neighborhood will notice it when they walk through your home.
I hope that helps and enjoy your new living space!
Keep in mind, the quality of the work and floor plan of your remodel will affect how future buyers view your home. If your remodel is not being done to code and without permits this could end up costing you when you sell.
Please make sure you are following local building codes for ceiling height. I believe they do have thinner duct work that can replace your current ducts and allow for more ceiling height.