So I read your post, OP, and a whole lot of the responses. And I just can't duplicate your experiences. At least for relatively basic computing tasks... which is mostly all I do on this little 12" MB. I do not notice any of the lag in programs you talk about. And this after I traded from an 8 month-old Late 2014 13" rMBP, with i5, 8GB, 256SSD.
In fact, I have gone so far as to run both the 12" rMB (1.2/512) against the 13" rMBP side-by-side and open web pages in Chrome and Safari. Open docs and files in Office 15 for Mac preview, messages in Mail, appointments in Calendar, add/edit in Contacts and spend some time writing/editing my docs in Scrivener. All of them--with the occasional exception of Office 15 preview--are very near identical. (Office does occasionally lag when opening a document for the first time. of course it also crashes sometimes too, but it is a beta/preview) I noted that you stated that you are noticing 1/2 second delays compared to more powerful Macs and I am honestly not seeing even that little bit of difference. (Though that would be hard to measure, I just am not feeling it.) My experience playing Flash video and things like YouTube has been stellar (have a YouTube video playing now, as I write this even.) I seriously wonder what the difference may be. It is also, possible that I am more forgiving and maybe I am truly not noticing such delays.
The Keyboard is subjective and you either like it or don't. I love it and hope they release an external model for the iMac. Yes I may have drank the Kool-Aide I guess when it comes to the new thin design and butterfly mechanisms, but I really like this keyboard! I love the click sound it makes as well and miss it on other Macs now.
Battery has been a mixed bag and has really varied based on the version of Mac OS X I am running. I am in the developer beta and run the various builds and some have made for great battery and others... not so much. I am currently running El Capitan DP1 and it has been... very, very, not so good. Abysmal even. I have considered going back to the last beta build of Yosemite just for that reason. But it's the software and not the rMB that is the issue. When I'm on a good build of OS X, I was easily getting 10 or more hours of battery.
So, again, not sure how your experience is so different. On the other hand, if you are used to more power and you run more complex apps, get the 13" Pro top-end model. It is heavier, but it is a great performer and you will probably be happier in the long run.