With one exception, all my batches for the last year have been 3- gallon. I have some 5-gallon plastic BMB's for primary, which are technically sold with the intent of being secondaries for 5-gallon batches. I also have some 3-gallon better bottles which I use occasionally for secondary.
While I see no issue fermenting 3 gallons in a 5 or 6.5 gallon bucket, I would assert it leaves too much headspace if you want to rack the beer off the yeast cake into a secondary vessel that big. A secondary is great for harvesting yeast, but otherwise the merits have been debated. So either get a smaller secondary vessel, or simply join the secondary debate on the "not needed" side.
The other benefit to 3-gallon batches is that it opens the door to stove top, indoor All Grain brewing. I use a 20-quart pot. Brew-day blizzard? No Problem!