Can you provide details of your connection? Do you have the transfer terminals? Will your baggage be checked through? Do you need to pickup another boarding pass?

There is one instance where I was transferring from a low cost carrier (Fly Dubai) to another more major carrier (JET) and it was pretty crappy. I used the "transfer" service to transfer my bag over and took a shuttle bus (read: un-airconed cramped van) to go from one terminal to the other. The bag transfer involved me visiting multiple desks and waiting for tons of documentation as they have a 3rd party service that does this.

When I get in the other terminal from doing this transit, I had to pass through security to get into the new terminal, pass through security AGAIN to get to the transfer desk, and then pass through security a THIRD time to get back into the main terminal area.

In the end, it would have been easier for me as a US passport holder to just clear immigration, grab my bag, and take a taxi/shuttle over to the other terminal, and go ahead and check-in/clear immigration.

After that I finished up with all this I went for a Kilkenny at the irish pub in the airport, which was very much needed after that transfer as well as the fact that I was coming from Saudi.