2*6V = 225 AH. In my books this is already better than 2*100 AH.
Some 12V batts - AGM in particular - hold voltage under load better than flooded 6V. Doesn't sound like you're considering AGM, so go ahead with 2*6V. Not that you have to replace them now.
"Higher charging voltage of 6V"? Sellers don't always know the products they are selling, not to mention products they don't carry. Check the specs. All batteries are different, some higher, some lower.
"Takes longer to charge"? Flooded batts have lower recommended charging rate than AGM, but this is true for all flooded. I doubt there is much difference in charging rate btw 12V and 6V flooded.