Would be nice if you combined Scrypt/Scrypt-N/SHA256/X11 rewards before payout

They are combined together. You just don't see that on graph.
I had this exact same suggestion a while back -- remember aggregated payout that I mentioned?
The key thing here is that the payout mechanism should check the
sum payout total of all the algorithms and check whether
that meets the threshold of 0.002btc instead of checking each one individually.
For example, say I have pending balance of the following for each of these algor: scrypt 0.0017, scrypt-n 0.00006865, x11 0.00046600. Even though scrypt-n is below the 0.002 threshold, that will
still get payed out on the next payout because the sum total of all three is 0.00223465btc. I don't believe the current system is doing that is it?
Payments are issued four times a day if your unpaid balance is greater than 0.01 BTC. Every fourth payment (once per day) is issued if balance is greater than 0.002 BTC. We will do payments for balances greater than 0.0001 BTC once every few days.
Payment threshold is checked for each algorithm even if you use the same BTC address for different algorithms. Each algorithm balance must correspond to the criteria above to be included in the payment. All balances for the same BTC address, matching the criteria above, will be combined into single payment.
Example:
User under BTC adress "xxx" has such balances:
a) Scrypt: 0.11
b) Scrypt-Adaptive-Nfactor: 0.04
c) X11: 0.0001
At the next payment round, total balance will be 0.11 + 0.04 = 0.15 BTC since a) and b) matches the criteria, however c) doesn't. User will receive 0.15 BTC in a single transaction. The X11 balance from c) will be paid in one of the next rounds, when it reaches the criteria above.
Note: We will implement a combined summarized threshold checking in the future upgrades to allow aggregated payout. It's in our TODO list we just haven't got time to implement it yet - it is not a trivial task since we have to do QA testing to make sure payments are 100% correct and exact.