This conversion program works well (for PLC-5 at least, never used it for SLC). I've used it along with the manual to convert very large complex systems. It's a great time saver, but given the choice I would always have liked to have used the original program as a reference to generate an "identical" ControlLogix project.
With the conversion utility, you get all of the old data tables (B3, N7, etc) created as arrays, and logic to hammer DINTs into INTs to make it work. It can't be expected to take advantage of what RSLogix5000 has to offer, and IMO The only "upgrade" you really get initially is the increased processor capacity.