As RMG mentioned, both HTTP and FTP are roughly equivalent in speed and reliability. In a TCP/IP network, each network layer has it’s own integrity mechanisms (for eg: checksumming). If you are using HTTPS, I think the SSL protocol uses checksums as well.
Some drawbacks of FTP in webMethods is that IS only supports receiving of FTP files via it’s FTP port - and does that very well - as soon as the FTP receive finishes, it invokes a service automatically. However, IS does not support spooling of FTP files for pickup by remote partners - for that you have to run a separate, non-webMethods, FTP server. Also, FTP uses two ports (in active FTP mode, as opposed to passive FTP), as compared to one port for HTTP. This causes possible timing issues which must be carefully addressed (for eg: partners logs into FTP server and tries to pickup file which is still being written to disk)
I hardly know anything about AS2 or AS3 etc, but it probably has well defined fields for digital signatures, non-repudiation functionality, etc. This is probably doable in HTTPS - but I don’t know much about digitally signing documents going over an HTTPS transport.
If there aren’t specialized protocol requirements (eg: you don’t need to interface with AS3 customers, etc), I’d go with HTTP.