I think one has to balance out the highly inflated rates (yen/points) during sakura season against what's really important. If it's truly the sakura, then buckle up and unhinge the wallet.
If sakura is not the true top priority, aiming for a trip just a few weeks later can be extremely rewarding. But that's a personal choice.
Odaiba Hilton has nice views of the skyline and the rainbow bridge, plus the Yurikamome line stops just feet away. Have never seen rooms but the ground floor looks decent enough.
Hilton Osaka is right next to Osaka station and Hankyu Umeda, so no shortage of options there. Easy to get to Kyoto for sure. Nara is a change or two but nothing horrible. The Hilton is nice, if not completely modern - the service I found to be quite good.
Personally, even though I have considered it in the past, I won't sacrifice a night in Tokyo for a slightly easier morning starting from Narita.
For your itinerary, open jaw return from KIX might be a better move. Repositioning to NRT just to leave - not sure that's a good spend of time/effort.
WRT to Limo bus vs. NEX in Tokyo - I find it comes down to this. The N'EX can be a hassle to get to, but once on, you're done. The bus can be easy to get onto, but things can (and have, for me) happened on the journey to the airport. The bus doesn't just stop at your hotel - it has a route and you'll hit 4-5 hotels and probably a train station before you set off to NRT. Two visits ago, boarded at Hilton Shinjuku, then made 3-4 stops, then stopped at Shinjuku station and once there, there were some 20 people with massive amounts of luggage to get on board. Went from a peaceful trip to a frustrating one very quickly.
Also, Limo bus from the airport to the hotel is nice - no surprises there. No worries about an overbooked bus, no schedule worries.