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Since I tend to keep my phones until they die, I'd recommend getting the newest one. It will be more future-proof.
 
What carrier are you on? If you're in the US, AT&T and T-Mobile customers should wait until the fall to get B14 and B71 support, respectively, on Sprint, even the iPhone 6 supports 25/26/41, while on Verizon, you'd want at least the 8 for B66. Keep in mind that each newer version has a higher category of LTE, which includes more CA, MIMO, etc, and that all carriers are deploying or will deploy 4x4 MIMO, which isn't supported in any current iPhone.

It seems that nobody pays attention to the LTE bands, but it does matter. Due to AT&T's spectrum position in NYC, it's an extreme example, but we were sitting at dinner in Little Italy, and my friend on AT&T was using an iPhone 6 or 6s, neither of which support B30, and his iPhone barely had working data, while my Galaxy S7 on AT&T was cruising along at 50mbps on B30. I saw the same thing with my ex's phone in Times Square, she was barely loading stuff, I had over 10mbps. The SE is a nice little phone, with without modern LTE bands, it's not that useful. I'm starting to feel left behind without B66 and B14, which are rolling out in urban and rural areas, respectively.
 
6s or SE.

Both have an A9.

Both will run iOS 12 fine. And if you’re lucky both may be okay on iOS 13, if you’re lucky. Neither will last longer than that.

Where’s the logic in that? A 5 year old A7 device gets supported but a on A9 device will be dropped after 4 years of support? 5s (A7) unlikely to keep support through to iOS 13 but the SE and 6s will likely get iOS 14 and maybe iOS 15 unless something crazy changes. Apple still sells new A8, A9 devices today. They aren’t going to obsolete them that soon
 
Ideally it's up to you, the newer models obviously get updated further in the long run, but the SE is great value for money and more than likely get another year or two of updates.
 
As others have said pretty much the 6s series (including the SE as it effectively is a 6s in the body of a 5s) the A9 and 2gb of RAM mean it’s not often you see them getting too sluggish even now they’re getting onto their later iOS versions. Considering Apple still sell the 6 brand new through third party channels I wouldn’t be surprised if the 6s continued being sold even after September, taking its place. Assuming Apple drops a chipset generation per year, we’ll see A9 devices get iOS 14 as their final version, so that’s still a solid 3 years of full support.
 
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