I realize this is a very old post and also a well-worn topic but, having just seen these two courses myself for the first time, I feel a compulsion to add my two cents.
There is no question that these courses are bound to be compared with each other due to proximity, topography, history and tradition. I'd bet that, like me, most people who are travelling to Ireland to play golf experience them for the first time during the same trip. Therefore, it's a natural comparison.
There's also little question that they belong in the same discussion in terms of the quality of the playing experience. They both have everything you'd want in links golf - the firm and fast conditions, the quirkiness and blindness and intimidating bunkers, the towering dunes and spectacular sea views, unpredictable and wildly changeable weather.
I guess when it comes down to comparing them though, it's a question of whether you like to ease into things and delay gratification or if you're the type of person who enjoys eating dessert before dinner!
Frankly, my first few impressions of Ballybunion turned me off and made it a little difficult for me to recapture my anticipation and excitement. The clubhouse is a bit of a monstrosity and reminded me of huge clubhouses in the US, not the rustic charm I was naively hoping for. As has also been widely discussed, you don't get a hint of the ocean or big dunes until you've reached the 6th green. I couldn't help but wonder if I'd come to the right place! Maybe the first impression wasn't helped by the randomly patchy marram grass that had been planted on the first five holes last winter. It hasn't established yet and looked a bit like hair plugs. Finally, the caravans and road adjacent to holes 1 - 6 were difficult for me to tune out, despite the excellence of the holes. Admittedly, these are all aesthetic impressions, unrelated to the actual golf holes but, you can't help but take it all in, can you?
Of course, when I walked off 6 green and looked down hole 7, I finally knew I was at the right place. Holes 7 - 18 were each more spectacular than the last - a wild roller coaster ride of golf! By the time I walked off 18 I was looking forward to the one hour ride back to Dingle, if only to decompress and reflect on those last 11 holes. Wow.
As for Lahinch, which I played two days later, the script was entirely flipped. The clubhouse and connection to the town were much more at the "right" scale and in keeping with my expectations. While the first two holes aren't the most spectacular, they were really good and holes 3 - 14 were unbelievable, perhaps the greatest stretch of links golf holes anywhere? Certainly within the conversation. After that, 15 and 16 certainly weren't bad, leaving a fairly lackluster finish.
I guess the point of all this is that the holes within the dunes for both of these courses are indisputably amongst the most spectacular, unique and memorable of any in the world (and the course rankings reflect this). It's the holes that aren't within the dunes that are comparatively disappointing. Maybe choosing a favorite between the courses ends up being personal preference - would you rather get the disappointment out of the way early, leaving yourself with the finishing impression or is the experience better if you're not initially let down and can get through the lackluster late holes riding on the momentum of that initial euphoria.