You are right that it's not good style to use the same preposition twice in a sentence. Sometimes it is unavoidable, of course, and so I wouldn't worry about it too much.
In this case there are two options. First, change "waiting for" to another preposition, like "waiting on". This might feel incorrect to some peoplefeel incorrect to some people, but to me it sounds fine.
Second, as FumbleFingers says in his comment, see if you can get rid of one of the prepositions. In this case you can say:
I've been waiting ages for you
Again, this is not always available so if you must repeat something, go ahead.