ASUS Prime B350M-A vs MSI B350M GAMING PRO

The two motherboards you are considering have these similarities:
Both are mATX format (but with slightly different widths)
Both have a single PCIe3.0 x16 slot and two PCIe2.0 x1 slots
Both do not support multi-GPU's (due to having only one PCIe x16 slot)
Both have 1x M.2 socket (supporting PCIe x4-mode or SATA-mode)
Both have the same Realtek RTL 8111H LAN Controller
Both have the same Realtek ALC887 Audio Codec
Both have 3x Audio Jacks at the rear panel
Both have a total of 6x USB ports at the rear panel (but different versions)
Both have 1x USB3.0 and 2x USB2.0 internal/on-board USB headers
Both have a Serial Port (9-Pin COM) internal/on-board header
Both have 1x +12V/G/R/B (4-Pin) internal/on-board RGB LED Strip header
Both require 1x 24-Pin ATX cable and 1x 8-Pin ATX12V/EPS cable from your PSU
Both have 2x out of its total SATA ports in a 90-degree orientation

The main differences between the two motherboards, Asus Prime B350M-A and Msi B350M Gaming Pro are:
Asus has 4x RAM slots (up to 64GB capacity) | Msi only has 2x RAM slots (up to 32GB capacity)
Asus does not have PCIe Steel Armor support | Msi has its PCIe slot with Steel Armor support
Asus has a total of 6x SATA ports (4x via Chipset + 2x via CPU) | Msi has a total of 4x SATA ports (via Chipset)
Asus has 2x PS/2 ports at rear panel (1x for KB, 1x for Mouse) | Msi has 1x PS/2 combo port at rear panel
Asus has 4x USB3.0 and 2x USB3.1 Type A rear panel ports | Msi has 4x USB3.0 and 2x USB2.0 rear panel ports
Asus has no Parallel Port (25-Pin LPT) internal/on-board header | Msi has 1x Parallel Port (25-Pin LPT) header
Asus only has 2x total fan headers (CPU_FAN + CHA_FAN) | Msi has 3x fan headers (CPU_FAN + 2 SYS_FANs)
Asus does not have any Debug/Diagnostics LEDs on-board | Msi has Debug LEDs (for CPU, RAM, GPU, and BOOT)
Asus is Gray+Black themed with no Ambient LED lighting | Msi is Black+Red themed with Red Ambient LED lighting
Asus is wider at 244mm x 240mm | Msi is narrower at 244mm x 210mm

Since the price of these 2 mobos are the same (almost), it will all boil to personal preferences on features that you need/want.

If you are planning to go with 4x RAM sticks, then the Asus is your choice.
If you need USB3.1 (Type A) USB ports at the rear panel, then the Asus is your pick.
If you need more SATA ports, then Asus has more.
If you want stronger PCIe slot (esp. if using large/heavy GPUs), then the Msi has it.
If you need diagnostics indicators (Debug LDs), then Msi offers this feature.
If you need more fan headers, then Msi wins.

Aesthetic-wise or color theme, also, is something to consider (esp. if you want good looks on a window panel case).

I'd go with Msi. You won't be needing more than 2x SATA ports, you won't be needing more than 2x RAM sticks, you have no idea if you need a USB3.1 rear panel port (the MSI doesn't have 3.1, but it has the same number of rear USB ports as the Asus), you'd have a Steel Armor PCIe slot (for avoiding breakage due to heavy GPUs), you'd get Debug LEDs, you'd have more fan connector options, and, aesthetically, it'll match your Spec-Alpha Black+Red chassis.