keg vs bottle taste difference

Over the past couple of months I've brewed 10 gallons each weekend, 5 going into a corny keg and 5 going into bottles. I start each 5 gallon batch in a bucket, then after a week I transfer the batch that I will be bottling into a glass secondary for an additional two weeks. The batch that I will be kegging I leave in the bucket for a total of two weeks before transferring to a corny keg. I force carbonate the kegs and leave them at about 40 degrees until I decide to tap them.

Since I started this 10 gallon routine, two batches have aged long enough to begin drinking them. What I've noticed is that the bottles in each batch taste better than the kegged beer. Its not that the kegged beer is bad, its just not as good. The only real difference between the two beers should be that bottled beers use priming sugar while the kegged beer doesn't (shouldn't make that much difference to the taste). And that the bottled beer remains at room temp for a total of 6 weeks (3 in fermenters, 3 in bottles), while the kegged beer goes straight to crash cooling 2 weeks after brew day. Now I'm beginning to wonder if my kegging schedule/routine is flawed. Should I be keeping the kegs at room temp for a few weeks before cooling them down? Or is it fairly common for either the kegged beer or bottled beer to be slightly better than the other and I should just RDWDHB?

I would say that for your comparison to be accurate enough to actually decide if one is better than the other, you need to condition both batches in exactly the same manner. As it is, you have no way of knowing if it is keg/bottle, or aging techniqes that are affecting the flavor.

I condition both my bottles and my kegs at room temperature with natural carbonation and I can't say I've noticed a difference in taste between two batches of the same recipe. Unfortunately I can't do a direct side-by-side because I can't do batches that large, so I don't know how useful that information actually is.

If you want to find out for sure, on your next batch, naturally carbonate the keg alongside the bottles for the same time periods and see how it turns out.

I have noticed the same thing. So far I haven't had a beer that I kegged that was as good as my bottled beer that conditions for an extra 3 weeks at room temp. I'm starting to think the beer benefits from the extra time at room temp.

It's also possible (likely? guaranteed?) that you aren't getting an exact match on the carb level between the kegs and bottles. And different carb levels can definitely affect your perception of a beer.