Complex Arduino programs
I noticed that it is very hard to use classes with the default IDE.
Each file will be in a different tab, but normally each class has a header (.h) and implementation (.c) file, so 2 extra tabs per class.

If you have just 3-4 classes you can use the default IDE.

However, if you want to use more, you have to use e.g. Eclipse or Visual Studio, whatever IDE you like best.

Search for Eclipse/Arduino, I think there are multiple options.

Myself I use visualmicro ... it is free except you cannot use the debugger option.

I used several classes in my sketch and don't think the compile time was 30 seconds; it might be depending also on the amount of include files.

Also a complex program is not necessarily a program with many classes. I would say, that if you put too much functionality in one class (or one single sketch), you get a complex program.