Unless you have a handheld radio where the antenna is mounted directly on the radio, it really doesn't matter what the connector on the antenna vs. radio is. There is no law that indicates that a piece of coax must have the same type of connector on both ends. It's quite common to have one type of connector on the radio end and a totally different type on the antenna end (think PL-259 on the radio end and an NMO on the antenna end for a very common ham mobile setup). On the commercial end using Motorola radios, you'll often have a mini-UHF on the radio end and NMO on the antenna end. You'll be hard pressed to find any antenna that uses the mini-UHF connector.
A good recommendation for your mobile install would be to get your desired type of NMO mount for the antenna (and a good dual-band NMO mount antenna like the Larsen NMO 2/70) and have the PL-259 connector on the radio end of the coax.
For a base install, one of the various base dual-band antennas (such as the Comet GP9 where you can opt for the standard SO-239 model of for lower loss select the version that uses an N connector) and make sure that your coax has the desired connector to match your antenna directly (the N male to mate with the antenna's female N if you select the N model or the PL-259 to mate with the SO-239 if you select that model) on the antenna end and on the radio end has a PL-259 to mate with the radio's SO-239.
Now, you'll also need some lightning protection and the connectors on that device will also need to be factored into the mix, and this can add some complexities. Many coax lightning protectors have standard female connectors on both sides, some with N and others with UHF (or SO-239), but if you don't check, you may end up with a male connector on one side and female on the other. This may sound crazy, but in many instances this is quite an advantage! Some of the better quality or more specialized models may use other types of connectors so it's important to check prior to ordering!
Let's say that you want the lowest loss and have an N type connector on your antenna. You also selected a lightning protector with female N connectors on both sides. Your radio still has the typical ham standard of SO-239. You'll need two runs of coax, one from the radio to the lightning protector (PL-259 on the radio side and a male N on the protector side). The other run will be from the lightning protector to the antenna and have male N connectors on both sides. It may sound complicated, but if you break things down to their basic parts, it really isn't all that difficult.
I do agree that it would be better if the mating connector used similar codes but we just have to learn that PL stands for plug and SO stands for socket (well, that part is somewhat logical anyway) and for unknown reasons the PL-259 mates with the SO-239. We also must know that the PL-259 and SO-239 are known as UHF connectors, which you'll often hear the pair referred to. You'll also have to ignore that those very same UHF connectors don't work all that well on the typical UHF frequencies (which is why the better designed N connector is often preferred). Clear as mud, isn't it?
