There is a national cycle route that tries to avoid (most) of the A9 by either cycle path or the parallel minor roads. The thing is, I don't think End-End riders know about it and I have seen a number of riders on the A9 which (in my opinion) a very dangerous road.
H
The Sustrans route is pretty crap in places too. I tried it for a short while in 2006 and gave up when it turned into a flight of stairs. Bugger doing that with camping gear/a tandem/trike/recumbent etc. Come to think of it, bugger doing that with a child trailer.
However, the climb up the Pass of Drumochter, allthough was twisty turny, narrow so more than 12mph was often too fast even when the track was clear, it's a lot more pleasant than the A9 if you're a slow rider not on a tandem trike (a tandem might manage) It's more fun than the A9 and worth slowing down a bit to do unless you need to get a move on, though you'd have to be pretty fast for it to be worthwhile using the A9.
The sections of old A9 are very nice. Some of them are "hidden" though I think they are marked with Sustrans signs and some of the old A9 goes through the towns. The Sustrans route seems a lot better once you get to the Pass of Drummochter all the way to Inverness.
Funny how people's ideas about roads differ. I quite like the A9 and prefer it to the A30.
Another alternative is further east, which involves a lot of arrowed climbs. Never tried that route myself yet. Last time I went that way I was on about a 95" fixed and didn't fancy walking so took a flatter route.
Or there is the western route, which is single carriageway A85/A82 over Rannoch Moor. The scenery is nice (especially Glencoe) but I don't like that road. On my way back from Scotland on my last trip I hung around Glencoe until evening so that I could do that road and get through Glasgow through the night, just to avoid shitty driving (close passes at high speed with oncoming traffic). I'd have much prefered the A9 YMMV You'd then have to go via Loch Ness up to Inverness which gets very busy and is a narrow single carriageway road. I've only done that once on my 95" fixed, so was shifting a fair bit, which makes heavy traffic feel not so bad.
It'd add on a few miles too.