if the size of flagstone steps you are going to use are big enough, I would mortar set one of them right over the skimmer opening (lid). I would then have your mason cut out a middle section of it for access.
It should most likely be reinforced underneath with a plate of some sort.
This plate would rest on the skimmer plastic to prevent this smaller piece from cracking when people walk on it.
Also check out pour-a-lids for an easier way to do the above.

Option #1 is doable, and I have done it many times on raised pools that have just 12" or less of coping only. The interior basket is smaller than a standard skimmer, so it needs to cleaned more frequently, but in my installs these pools have been raised so they see less leaves anyway. good luck!

We used a company called www.pouralid.com. The product was designed for pouring concrete or aggregate into the lid to match the pattern of your deck but others have used it to put stone work onto it. It has a benefit over just laying a loose stone over the area because it comes with a ring that you can still mortar or sand around to prevent the rest of the stone or paver finishes to be loose and the resulting cover already has convenient finger holes to grab the lids off.

Here's an example of someone else who used it who posted here. Scroll about halfway down for the example pictures. And these lids were super inexpensive (about $20 for each skimmer).

http://ths.gardenweb.com/forums/load/pools/msg082238171106.html

Good luck.

Thanks for the link to the photos. They look great!

Thanks for the link to the photos. They look great!

Hi Idjd,

Better late than never: the answer to a great skimmer lid is at: www.skimmerlids.com.au

The QUAD lid helped us sort out our problem and very helpful staff too.