Definatly patch to SH3 1.4b, and use JSGME to enable your mods.
I would play at least a few patrols in the plain game to get a hang of it, and you wont know if you like the changes in mods if you don't know what the mod mods :hmm:
SH3 Commander doesn't really change anything in-game too drasticly, though it will let you costomize a lot of settings to your choosing. Commander is a seperate program, not a 'mod' as such, so you wont need to install it with JSGME. It lets you see a great display of your players career history, change settings (you choose time in base between patrols, crew transfers, deck gun reload time, etc)
I love RuB, but I would still recommend you have a few missions in the stock game before trying any of these type of mods.
There's also plenty of graphical mods to choose from, just pick the ones you like the look of.
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