Honda isn't that small. Wikipedia the All-Knowing lists him as 180 cm. That's taller than our defensive midfielders Flamini and Gattuso (and just 2-3 cm less than Ambrosini). He isn't that skinny either, so he should perform well even in physical games.
Now I haven't seen him much, so I cannot vouch for his defensive qualities. Nonetheless, his work rate is so high it can almost compensate. And he is young and seems quite clever, so I'd say Allegri can improve him considering what he has done with Abate who doesn't seem to be the smartest bloke around. With two runners like Honda and Boateng, we can afford to play only one true mediano (Bommel) since they can both compensate for lack of pure defensive skill with running. The midfield Ca Rossonero suggested could very well work:
------------CAM--------------
Honda--V.Bommel--Boateng
The question remains who we should get as CAM. The names right now are Ganso, Hernanes, Lamela and Pastore.
Now consider that depending on the game at hand, we would still have some valid mediani on the bench. Flamini will most certainly stay (see nefremo's post) and so might one of Ambrosini and Gattuso (given the offer at hand I'd probably let him go). If we want to opt for a more defensive midfield we could push up one of Honda or Boateng to the CAM position and place a mediano in the midfield trio. Actually maybe even two of them, even if that would probably not solve any problems. Anyway, the point is we have valid options.
I still want to stress the importance of Galliani's statement that we have too many players at the moment. We have 31 players and we want to reduce it to 25-26. This is the situation accounting for Mexes, Taiwo and the 2 midfielders:
GK (3): Abbiati, Amelia, Roma
DF, C (7): Nesta, Silva, Yepes, Bonera, Papastathopoulos, Legrottaglie,
Mexes
DF, R/L (7): Abate, Zambrotta, Antonini, Oddo, Jankulovski, Didac Vila,
Taiwo
MF (12): Ambrosini, Gattuso, Seedorf, Pirlo, Flamini, Van Bommel, Boateng, Emanuelson, Merkel, Strasser,
CAM/Trequartista,
Creative Midfielder
FW (6): Inzaghi, Zlatan, Pato, Robinho, Cassano, Oduamadi
The grand total is 35 players. And yes, players like Strasser and Oduamadi count on the list.
We therefore have to lose 9-10 players. And for every other player we want in, one has to leave (I'm expecting just 2 big signings though).
The obvious deadweights are Jankulovksi, Legrottaglie and Sokratis. These guys should almost certainly be sold, even for peanuts. Maybe Sokratis loaned. Vila should also be loaned, unless management/Allegri have high hopes for him (which I doubt

). Then there is Bonera. Is having 4 dedicated/pure CB's enough? In any case it might be nice to have someone versatile like Daniele, albeit awful at times.
So from that block of players we can/should realistically free up 4-5 players through sales or loans. We probably wont earn much, although Janku's wages are quite high.
Then we have some youngsters. Merkel, Strasser and Oduamadi. I would loan out the last two. Merkel seems ready to play some more games for the first team. So here we lose another 2 players.
Now the tricky question; i Senatori. To me Nesta is an obvious keep. Inzaghi too. THe question revolves around the mediani Gattuso, Ambrosini, Seedorf, Pirlo and Van Bommel (isn't really a true senator, but still falls into that category).
Considering we freed up 6-7 spots with the previous categories, we should be okay with letting 2-3 of these guys go, assuming we just reinforce the midfield with two men. It's really up to the management who to let go and it also depends on who we end up signing.
Gattuso and Pirlo, though, are my most instinctive players to let go. They are also the ones we really earn money on and the most realistic ones as things stand right now.
Seedorf is a tricky question. When he is motivated he is one of the best midfielders in around. When he is less inspired, he gets boos from his own fans. Will he be motivated all year long? Hard to say. We should add that he nonetheless requires two mediani to function properly; we've all seen him and Pirlo play together this year. It would be good to let him go when he is on top. As much as it hurts, it's better to part with such a good memory of him than seeing him walk his way around the field for 90 minutes. The problem with letting both him and Pirlo go, however, is that we will lose two very unique, creative and technical players hard to find.
Van Bommel I would keep. He has always done well, despite his aggressive tendencies. An incredibly smart player. Then we have Ambrosini. I feel like he's sometimes underrated by the fans. He still does his job and he is the captain after all. Add the fact that he earns less than the other Senators ("just" 3 mln) and that we can probably half than with his new contract, and I don't see why we should drop him.
I trust the management will do the right job, considering they said they want to invest and take us to the top of Europe. The key is getting rid of the deadweight, loaning some youngsters and finally making the right choices with the Senators.
P.S: Wow, sorry.... that post turned out longer than expected