My fiberglass isnt bad, but its not what I want.  Still fair luster, but inconsistent shine across the deck. Variation from earlier attempts to hand polish/wax.  

Even a trained eye will have a hard time telling for sure exactly how aggressive one needs to be to restore gel fully. I’ll counter Chris’s advice and suggest you do the opposite. I always do a test spot (starting from least aggressive to most aggressive) to figure out exactly how far I need to go. Preventing extra work is a good thing. I do think it’s likely you’ll need to compound, though.

What material is your cover made of?

For some reason i can't post pictures. Good friend a pro glass guy told me to use a product called vibra cut from a company called fountain of youth.
I follow up with vitro from the same company or collinite 885 fleet wax.

http://www.power1one.com/Fountain_of_Youth-Home_of_Power_One/FOY_-_Vibra_Cut.html

Wet sanding buffing waxing are beyond my skill set and have to use hi quality materials to make up for the lack of ability.
Howeved i just wrapped up a seat project ( clear gelcoat over carbon and carbon-kevlar hybrid)
The gelcoat was applied last and wet sanded then buffed & waxed. Shines a mile deep.

It also completely brought back a deep shine on original white gelcoat on the 79 nautique project i finished 6-8 months ago. Swear by the stuff because it makes me look good.

I have a Makita variable speed polisher, 8" with a nice wool polishing pad.  ( I tried the foam pads and went back to the Wool, personal choice)  I wash the pad between each type of compound used.  Well, wash is an exaggeration, I spray it out well with a hose spray nozzle and then spin it to remove the excess water.   I have been using a 3M product, they sell a kit with the Step 1 course, Step 2 Medium grit, and Step 3 Fine grit compound.   (available on Amazon) I spin at a lower speed for all 3 finishes.   I am not a pro, and far away from being any kind of finish expert but it allows me to get great results.   I wish I had Tim's advice when I started, it makes total sense to figure out how much material you need to remove on a small area before putting in all the work on a larger area.   When you start the first step takes away any shine you have and you won't know if you have the proper amount removed till you try and polish that spot.   It is a learning process with the constant fear that if you remove too much you might take off your Gel Coat Color.   I did that once polishing my old Malibu Skier taking out a scratch.  Nautique uses thicker Gel than Malibu but always be careful.  The 3M kit gives you a full Quart of each compound and other than shaking it before each use has lasted me years.   I think it is around $150 for the 3 but worked for me on a few projects now.  Even polished the headlights on a couple cars to remove glaze and it worked the same.

I would recommend a breathable cover if you ever put it away wet (ie, use a ski boat as a ski boat). I think the sharkskin is a poly based cover, not sure if it would be considered breathable like sunbrella. I am pretty sure I had one once, was not a big fan.