Gigabyte GA-Z97X-GAMING 3 has better VRM than MSI Gaming 3.
MSI Z97 G45 will be the best option among both.
If you dont plan to make a multi-GPU setup, less PCI-e slots means nothing. As far as I know Gaming 3 doesn't support SLI but it supports Crossfire. Still it has 1 Gen3 x16 slot and 1 Gen2 x16 slot. Also it has fairly weaker VRM. Still enough for mild overclock around 4.4 Ghz though but the VRM will heat up a bit, since it has 3 true phase design in real but with the use of doubler driver they made it look 6 phases. All of the manufacturers do that actually.
MSI Z97 G45 and MSI Z97 Gaming 5 has 4 true phases analog PWM design doubled to 8, 8x On-Semi Powerpak MOSFETS which are decent and 8x High quality 60 AMP inductors. Unless you are into breaking overlocking records, this VRM is very capable. But not the best in this price range. (for instance Gigabyte Gaming 5 has a better VRM overall)
If you really don't plan to use an M.2 storage device in the future or upgrade your cpu to a Broadwell (8 chipset might support broadwells though but we still not sure) Z87 would do the trick for you. But there are also some minor advantages of Z97 boards. No doubt that manufactureres found some time to enhance their designs and optimize the power regulation further, since these two chipsets are really the same in the heart. I don't think that would effect the overclock potential of the board though (since most of the times you are limited by your CPU chip) but it would effect the stability, power consumption and efficiency for sure. So I'd always suggest a Z97 board.
Z97-G45 is a decent board though and can handle a 4.5GHz overclock without a problem. But if you can pay a little more Z97 Gaming 5 would be a better choice. Also it has slightly better onboard solution. Both has Realtek's ALC1150 Codec though, but this time around MSI employed a really top notch Nichicon audio Caps for Z97 gaming series motherboards. These Caps are the ones that are used on studio grade equipments.