It may indeed be cheaper to buy larger panels, with more total output than needed, and accept the fact that a significant amount of that power will be lost due to shading, than to buy smaller "RV" panels that eliminate shading altogether. I don't know... I've never priced panels that I knew would be shaded if I installed them. I'm with Desert Rat though... it would drive me crazy knowing that I was wasting so much power and roof space.
With 1100 watts of partially-shaded panels, at more northern latitudes in the winter, you could probably get by with a 60 amp controller. However, in the summer, in direct sunlight, I'd recommend at least an 80 amp controller. Shading isn't going to be an issue, and controllers emit a fair amount of heat while operating. A 60 amp controller is going to be overloaded in direct sunlight with 1100 watts of solar in the summer.
Our FM-80 (80 amp) is basically just an FM-60 with a self-regulating cooling fan, but that fan kicks on all the time - even in the winter. In the summer, it runs almost non-stop while the panels are charging - and that's with 960 watts of unshaded solar.
I am just throwing this out for consideration.
I have 1500+ watts of solar panels and use 4 charge controllers, ( two 40 amp and two 30 amp controllers).
Blue Sky has a networked IPN system that allows for adding multiple charge controllers up to a couple hundred amps.
I also have three seperate battery banks although the network would support combining them into one large bank.
In the link that I posted I mentioned using the Blue Sky Network configuration. One of the charge controllers acts as the Master Controller and you can add several 40 amp networked MPPT controllers to increase the charging capacity up to well over 200 amps. This system allows for expansion as you add panels or you can set up the full charging capacity up front. One of the benefits is that each charge controller is wired separately and can feed either a single large battery bank or separate battery banks.
Using this network you can maintain a large 12 volt system or several systems and distribute the weight of the batteries rather than having too much tongue weight as mentioned before.
You might want to do some research on the Blue Sky website.
Edit:
I just copied this explanation from the manual.
INSTALLING A MULTI-CONTROLLER SYSTEM USING THE IPN NETWORK
The 3000i may also serve as an IPN Network Master controlling up to 7 remote IPN Network compatible Slaves. Any Blue Sky Energy charge controller capable of operating as an IPN Network Slave may be used, and as of this writing include; SB3024i SB3024Di, SB3024iL SB3024DiL, SB2512iX, SB2512iX-HV, and SB1524iX. Another 3000i cannot be used.
Controller types and their PV modules may be different. Each controller is installed as a separate standalone charging source connected to the battery and are then networked together. The 3000i serves as the charge control and network communication Master, controls the charging process, and directs the activities of one or more Slaves. No additional communication hardware or software is required to setup or operate the network. A network communication link is established between controllers by daisy chaining a twisted pair cable from the IPN Network terminal block, controller to controller (A-to-A, B-to-B) as shown in Figure 6. Up to 8 IPN based charge controllers can be connected together in a multi-controller system. The 3000i is fixed as device address 0 (zero) and serves as the IPN Network Master. Attached controllers are configured as Slaves set to addresses 1 through 7.
If an optional battery temperature sensor is used, only one is required and it must be connected to the 3000i (Master) to be recognized and shared. Optional displays or UCM may connect to any controller on the network.
As I understand this system you could use a 3000I (30 amp mppt) with 7 SB2034iL controllers (40 amp) for a combined charging of 310 amps.
The Charge controllers are not very big. The pictures are in the linked post above, one of a 2034 and the other of a 3000I and a network monitor.
A good analogy for this method of charging is that instead of having a fire hose filling a swimming pool you have several garden hoses. (ie several smaller cables rather than one monster cable).
Another advantage is that a shadow or other problem will only effect the controller output for those panels shaded even though the Master controls all the slave controllers.