Currently, paying a fee is controlled manually with the -paytxfee switch. It would be very easy to make the software automatically check the size of recent blocks to see if it should pay a fee. We're so far from reaching the threshold, we don't need that yet. It's a good idea to see how things go with controlling it manually first anyway.
It's not a big deal if we reach the threshold. Free transactions would just take longer to get into a block.
I did a rough tally of 4000 blocks from around 74000-78000. This is excluding the block reward transactions:
There were average 2 transactions per block, 17 transactions per hour, 400 transactions per day.
Average transaction bytes per block was 428 bytes, or 214 bytes per transaction.
The current threshold is 200KB per block, or about 1000 transactions per block. I think it should be lowered to 50KB per block. That would still be more than 100 times the average transactions per block.
The threshold can easily be changed in the future. We can decide to increase it when the time comes. It's a good idea to keep it lower as a circuit breaker and increase it as needed. If we hit the threshold now, it would almost certainly be some kind of flood and not actual use. Keeping the threshold lower would help limit the amount of wasted disk space in that event.