It's not just flickr....
I was also annoyed when my BT Internet email became BT Yahoo and they moved my email over to what is effectively a Yahoo account without the ads.
I don't mind it too much as they have a nice webmail interface, but it would have been nice to be able to say sod-off I'll keep my POP3 non yahoo account thanks... if they had kept it separate it wouldn't be possible for yahoo's vulnerability to affect the safety of my email account! (although the password is suitably high-strength, so it should withstand a brute-force attack for quite some time hopefully).
As for the flickr logo, yes I think it's an eyesore too... but frankly, I had more annoying things on my mind when I saw it, it does ruin the style of the flickr homepage though.
(I can't complain too much though, as it was the BTInternet -->BTYahoo change that gave me free flickr in the first place! :) )