That is a really difficult question.
I could say, just pay the big bill, but in truth you SHOULD be allowed the exclusion since you fit the situation intended, other than having the deed properly listing you as part owner.
I have to suggest you see a local real estate attorney for advice.
Having your name on the Deed is the best way of proving ownership, but you and your brother may have had an agreement where you can legitimately say you owned the home two of the last five years.
I am not an attorney, so I can't make that call. But I do think that as far as the intention of the tax law, the exclusion is written for someone in your situation, had the house a long time, used it as your home, now selling it and making a profit, so you should get a break on the capital gain.
See if there is something you can get as documentation to prove prior ownership if the IRS asks.
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