It really depends on what part of Tokyo you're staying in. To my mind, the fewer transfers, the better.

I like to stay in the northern part of Tokyo, which has more of a "neighborhood" feel than the parts around Tokyo Station, etc., but on my last trip, I was leaving on the Shinkansen for Hiroshima on the day after arrival, so I booked a hotel in Shinagawa and took the N'Ex.

Normally, however, I take the Keisei line, because I stay either in Ueno or just a couple of stops away.

I never stay at the kinds of hotels that are served by the LimoBus, so I haven't ridden it since the olden days, when you could go through exit procedures at the City Airline Terminal and be officially out of Japan the minute you stepped on the bus.