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Depends on your usage. If you're gaming jitter is probably worse, as it makes interactions inconsistent and jumpy in extreme cases. If you're downloading or browsing high jitter isn't much of an issue, it'll be overall faster if average latency stays lower. Unbuffered VOIP is another jitter sensitive one, particularly as your ears have much higher temporal response than your eyes.

I've never found base latency to differ much between ISPs, as there are many factors that can make latency higher than the minimum but none that can make it go below the minimum, it's just a question of how much above base each ISP stays.