There are advantages and disadvantages. One big plus is the cost. You can build top bars easily. Frames are much more difficult to make. If you use scrap lumber to build the hives and bars you could have a hive for just the labor. if you use a sheet of masonite soaked in water, dipped in wax to make blank wax starter strips you don't have to buy foundation. In a top bar hive you still have the advantages of comb manipulation as opposed to just having bees in a box and combs every which way. If you want cut comb honey or you want a lot of wax, then top bars work pretty well.
TBH Pros:
Cheap. If you put it in a trough hive at waist level (which most TBH's are but you could do with frames also) then you don't have to bend over or lift so high.
Easy to build.
More natural. The whole 4.9mm vs 5.4mm cell size is more of a Lanstroth frame hive issue. Most TBH users only do starter strips and the bees build what they want.
TBH Cons:
The frames are easier to break loose if they are burred or cross combed. If you are not careful with a TBH you'll beake the comb loose from the top.
The frames are easier to manipulate than TBH's. You can't flip a TBH comb sidways or it will break off from the top. You have to be more careful.
You can't extract easily. The combs are, as already mentioned, much more fragile because they are not reinforced with wire, they are not reinforced by a frame around them and therfore they break easily. You can't spin them in an extractor. It is a big advantage to have some drawn comb around when a brood nest gets honey bound or you're trying to start a new hive.
The old timers who write ABC XYZ of bee culture and the other old books, were trying to get people to stop using what they percieved as "old fashioned" practices. They believed that beekeeping should progress into the 20th century. Extraction, frames, standardization, modularization were the future. This is their perception.
My opinion is that frames are easier to work with. Frames are more advanced technology. You have to be more careful with a comb on a top bar, but I like the self sufficiency of being able to make my own. If you like simplicity and self sufficiency top bar hives make sense.
There is nothing wrong with a top bar hive. I assume you've seen Satterfields web site.
http://www.gsu.edu/~biojdsx/main.htm
There are a lot of good links here also.
I have done something similar to what you are doing. I built a long box of Lanstroth dimensions so I can put frames or top bars in it. Mine is as long as two Lanstroth boxes (21 frames or bars) and put it on a table that acts as a bottom board and I use deep boxes behind it as supers. The bottom board is 19 7/8" wide so the boxes go sideways from what a Lanstroth usually is.
I have also built one long hive the size of four Lanstroths, but haven't put any bees in it yet.