I was thinking march 27th till April 7th; 7 days in Tokyo and 4 in Kyoto. I thought this will be the best time to see the cherry blossoms...any thoughts?

Also let's say budget is not an issue, would you vote for any of the hotels next to the impartial palaces?

That's more time for Tokyo and less for Kyoto than I would want, but then, it's not my trip. ;-) It really depends on what YOU want to see and experience.

Where to stay is also a matter of personal preference. For my particular interests in these cities, staying near their respective imperial palaces would <u>not</u> have been a good plan. Your trip, your call.

What are you favorite areas that you enjoyed staying nearby?

For my interests in Kyoto, I prefer to stay in the Kawaramachi district.

For my interests in Tokyo, I prefer to stay near Ueno Park and its museums or in Asakusa.

JMO.

Please note that the OP has another thread going:
http://www.fodors.com/community/asia...oto-timing.cfm

Would it be better to stay in tokyo first or kyoto? I am coming from Seattle

Have you checked the cherry blossom predictions?
http://www.japan-guide.com/e/e2011_when.html

In Tokyo, I like staying in Asakusa, especially on our last trip this April - Asakusa was more lively than it was during a previous stay there a few years earlier.

We have also spent a couple of nights in Shinjuku, our first two nights in Japan on our first trip in 2012. We liked it as a first place to stay, though it might not be my choice now. If you have 5 nights in Tokyo, you could easily do 2 in one place and 3 in another.

Didn't love Tokyo Station as a location, personally.

In Kyoto, I also prefer Kawaramachi and my usual choice is close to the cross between Kawaramachi Dori and Sanjo Dori. It's good for local buses, local metro, there are lots and lots of local restaurants and bars within walking distance, and shopping as well.

I have booked the palace hotel in Tokyo and it looks pretty good. I will report when I return...