One of the great debates in Irish golf is: 'Ballybunion' or 'Lahinch'? People fall on one side of the fence or the other, with only a few caught in two minds. As others have suggested, try your best to play both so you can decide for yourself. It WILL be worth the effort. I favour early morning tee times but, given that this is the west of Ireland, you might find the sun setting over the Atlantic rather captivating in the late evening.
If you're playing as a single, I'd suggest phoning (rather than internet booking) clubs and asking to be added to a group... preferably locals. Local knowledge (or a caddie) will make all the difference to your enjoyment.
As for being off 17 and comments about the rough - you just have to persevere. It's links golf and it is what it is. I'd be a bit surprised - given the foot traffic - if they don't keep the rough thin/down to ensure balls are findable/playable.
No one has mentioned Ballybunion's 2nd course - the Cashen. It is routed through even bigger dunes than the Old, and while the oft cited complaint is that it is not a true links (designed by Robert Trent Jones) because of its target-golf greens, the back nine are epic (
some photos here). And it won't be nearly as busy - most American tours seem to skip it.
Dooks and Tralee and Waterville all battle it out for the most beautiful setting of any Irish golf course. Personally, I don't think anywhere can compete with the 2nd green at Dooks. 360 degree views of heaven. That said, your wife will definitely enjoy a walk around Tralee Golf Club.
If you want a non-links alternative, then try Killarney's Killeen course. It's an epic setting on a lake and under the mountains and this is an Irish Open course, so the maintenance will be top notch.