hmmm - a lot of distilleries offer tours, so I'd be tempted to either go for an area with a large number of distilleries (e.g. Speyside, Islay), or go visit your favourites. But remember that a lot of distillery's production may go to blends, so only be available through specialist suppliers (e.g. Gordon & MacPhail do a very wide range - Caol Isla would be an example of one which is mainly used in blends, and doesn't have a brand per se), so visiting the distillery could be a good opportunity to try some of these rarer ones..

you might find http://www.scotchwhisky.net/distilleries/index.php a good resource - there's a map of all scottish distilleries, and it also tells you what the visiting arrangements are (although some of it may be out of date ). Personally, i've only been to two - Bowmore and Edradour (the smallest distillery in Scotland). Both were interesting, probably Bowmore was the better visit, nice location - but also harder to get to!

If you are really travelling that much, wouldn't it be better to go visit one from each of the major groups

e.g:Islay - Laphroaig or Bruichladdich or Bowmore
Highland - Edradour or Glenmorangie (although a long way north) or Glenturret
Speyside - choice of either one of the biggies (e.g. Glenfiddich, Macallan, Glenlivet - well chose a name you recognise) or try some of the smaller ones used for blends -e.g. Dalwhinnie, Glen Keith...
Lowland - Glenkinchie
And for island, would depend if you got out onto any of the whisky producing islands... you mention Skye, so presumably Talisker would be a possibility.

Just a few suggestions - sure you'll have good fun planning it, and I would say pre-visit homework (ie tasting ) is essential