Remember also that you can get up to a 26% discount on a bulk buy of new planes - if you order enough and pay up front. So then, they will very often be cheaper than used ones even BEFORE you take the running costs into account.
Not enough used aircraft available when you want to order them. In the "real" worlds the best aircraft disappear more quickly.
Piece of mind, planning, strategy - knowing exactly what you'll get and when you'll get it - even 8 or 10 years in advance.
You can order the exact seating configuration you want at very little extra cost. Re-configuring old planes can be (relatively) expensive.
The used aircraft may not have the exact engine choice/range you want. You can end up with a complicated patchwork fleet.
Tax planning. When you make a large profit you really need to spend a lot of money at year end to save tax, so you effectively get a further 20% to 30% discount on that large order.
There is a (quite small) advantage to having a newer fleet apparently. I believe it affects your company image and if you play in an alliance it also affects that.
Sometimes, even if there are 50 or 100 of what you want available, it may be to your advantage to keep a production line open so you can buy more later. So ordering (I think) five new aircraft keeps the line open for another 9 months or so.
When you have a REALLY big airline, or when you open a new base for example, three aircraft a week is often just not enough. If you're ordering from 4 or 5 production lines as well as taking used aircraft you can grow at an impressive rate - 5 or 6 a/c per week.