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The biggest differences he talked about was PADI being more expensive and more time spent on manual dive tables.
PADI is the largest dive certification training agency worldwide. Mostly what that means is your c-card is more recognized everywhere.
Start with a basic Openwater Certification and proceed from there.
I don't see anything I don't like about these guys - and they're in Topeka - obviously no personal experience with them.
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They also teach TDI/SDI which can be a more technical certification so ask someone there which they recommend for you.
More important than the certification agency is the instructor so ask to meet theirs and pick one you like. In your market choices may be limited.
I think Beaver Lake in NW Arkansas might be your closest decent diving. I know divers in Wichita and that's where they go.