Sysdeo runs using your original CATALINA_BASE files (conf directory and so forth). WTP copies
selected files from your CATALINA_HOME and makes a new internal CATALINA_BASE inside a "server" project it creates. It doesn't copy ALL the files, which has cause me much grief. Additionally, instead of preserving application contexts, it's fond of modifying its copy of server.xml, which is something that's been discourage for a long while. Allegedly, if you override certain defaults you can prevent that, but it shouldn't be default behaviour in this day and age.
Tomcat, like most J2EE appservers, is a
Java Application. Like any other Java Application, it can be started with its internal debugger switched on. Eclipse can then debug it (and its webapps) using the Remote Debugging facility. That is, in fact, what happens when you run WTP or sysdeo, except that they make the necessary connections and setting for you, as well as starting and stopping the server for you. In the end, it's simply a question of who has to do all the grunt work, and I'd prefer it to be the computer, since I have work enough already. However, during the time when I'd given up on WTP and hadn't had any success getting sysdeo running, I had no choice.