As another IT person I definitely agree that the inability to pass variables and parameters to the command-line is a major issue since this effects putty, rdp and really anything where you have a single executable that requires a parameter.
I realize this use case probably isn't there for the average user but rather an IT user who often has many, many more passwords than most people. I think getting this to work for us is particularly important considering that it's the IT users who will quite often be driving your Enterprise sales.
I was pushing my organization to go with LP and I still may simply as a password vault but I must admit I'm rather disappointed in "LP for Applications" for the IT user. I could see it working somewhat for the general users though.
I think we are actually talking about two different uses; One is responding to a command-line prompt such as username/password whereas the other is simply storing and executing a command-line that contains variables and parameters. I can see that responding to command-line prompts would be a thorny issue but the case of issuing a command-line with specific parameters doesn't seem like it would be that difficult.
Could the problem be that you are trying to use a hammer to pound a nail and drive a screw when you really need to use separate tools to get the job done properly? (LP for Apps, issue a command-line statement with parameters, respond to command-line prompts respectively) i.e. "LastPass for Applications" fills in fields in GUI apps and then you have another tool called something like "LastPass CLI" that just issues a stored command.
Hmm... Slight tangent but how about "LastPass Scripter" that would securely store an entire script and be able to execute it. This could be used to replace all sorts of batch files and scripts as well as handle the Putty/RDP cases.
This all seems very simple to me... but then I'm not really a programmer.