I am a student of Shotokan, but realize like all MA's it has both strengths and weaknesses. Any ideas on which MA is a good compliment to Shotokan? Thank you.

If you can describe for me it's strenths and weaknesses (I know nothing about Shotokan), then I can recommend a complimentary style.

im currently doing shotokan and ICHF Hapkido.

Shotokan is great for striking moves, but i like the locks and throws of the hapkido.

Each teacher is different, but Shotokan is primarily a striking art. Therefore, to help to round out your game a bit more, you may look into some grappling style, like Judo or even Wrestling.

Just a foot note to what bushido_man said. Taking wrestling with a striking art is a great circle. Its great defencive practicality and wrestling is great fun.