This question prompted me to a thought: On at least one stack, I have sufficient rep to VTC. However, there are occasions when I think a question may be ... um, “questionable”, but I'm not really confident enough to say unequivocally that it should be closed. Perhaps there should be a difference for users with sufficient rep, where VTC says “I definitely think this is beyond allowable; close it.”, but flagging says “This looks questionable to me, but could be argued that I’m being overly suspicious; please, Mr/Ms Moderator, look at it.”.
What might help is to post a comment why you think the question might be closed. You can start from a close reason, e.g.
Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question.
and modify it to match your exact needs. There is a chance that the author of the question will read the comment, improve the question and it doesn't need to be closed after all.
It's worth noting that it takes (usually) 5 users to actually close a question, so 4 other users need to agree that the question must be closed as well. If you would flag instead of vote to close, this would be 5 users, so not much of a difference. As @ShadowWizard notes in the comments, you can always retract your close vote if you change your mind.
Alternatively, you could create a secondary 'sock puppet' account, have it gain 15 reputation (necessary to cast flags) and use that to flag the question. Be careful that it shouldn't interact with your main account, from the obvious "don't upvote each others' posts" to "don't cast a close vote on a question you've flagged with your other account".