Whilst I agree that a lot of current games will perform the same on an i5 there is an increasing trend towards newer games, especially console ports, demanding an i7 (or Xeon) to play on ultra. This trend is sure to continue and if the OP has no plans to overclock then they would be better investing their money into extra threads. After all, the price of the Xeon is almost the same as the i5 4690K anyway.
Some examples are The Evil Within and Watch Dogs plus there are some multiplayer games like BF4 that will also utilise the extra threads.
As for the motherboard, the price between the ATX and mATX H97 Pro4 is very similar so if you think you'll need the extra PCIe/PCI slots go for it!