MacBook – Why does BBEdit look bad with retina display

It is impossible to deliver an "answer" to this question. You are asking for something that is purely opinion-based. I have friends who use super small fonts and it's very comfortable for them. I also have friends who use larger fonts, and that works best for them. I personally use a variety of font sizes depending on what Mac I am on and what App I'm using. Your best best is to work with whatever font size suits you, despite what anybody else tells you.

There is no "one-size-fits-all" answer to your question.

Apple announced in the 2012 WWDC Keynote that applications needed to be updated to take advantage of the Retina display. Apps calling Apple text display APIs may benefit from Apple's improvements thereto without needing to be updated. Apps that use routines that had not been updated would use pixel doubling, which would make their text display using half the resolution of apps properly designed for the new machine.

Apple, naturally, has updated many of their apps, but the versions of third-party apps on the machine you tried had likely not been updated.

There is little you as an end user can do to make the programs render text better, but if you are using products from reputable vendors who update their products frequently, such updates should be released soon to take advantage of Apple's new HiDPI settings.