Have you got stagger?
At various times in its long history, the Stratocaster has shipped with staggered-height pickup poles. Actually, the Tele has too but much less frequently.
The 'why' of it is easy. It's intended to balance the output of each string so that one isn't louder than the next.
The staggered pole pieces attempt to accomplish this in two ways:
1. They compensate for the radius
The fingerboard on your guitar neck has a 'radius'—it's not flat but curved like a cylinder. If your guitar's set up correctly, your strings will follow this radius from 1st to 6th. So, if your pickup pole pieces are all the same height, those in the 'middle' will be a little farther from the strings and may pickup a little less of the string's vibration.
Having the pole pieces in the middle of the pickup be a little higher means they are the same distance from the strings as those at the outside.
"Ah," I hear you say, "But my Strat's pole pieces are up and down in some crazy pattern."
That brings is to the second way a staggered pickup tries to balance things:
2. Compensate for string size output
A magnetic pickup works by sensing a vibrating string in its magnetic field. The size of that string affects how much of a signal the pickup will output. The funny stagger of those Strat pickups is intended to match each string's output.
Now, even wrapped/wound strings have a solid core and that plays a big part in determining the string's output. This is why the staggered, up-and-down pattern seems weird when you first look at it. The stagger is matched to each string's relative output rather than the apparent physical size of the string. An unwound 2nd string can have more relative output than an apparently bigger 4th string, for instance.
As with many things in the guitar world, the problem is 'history'. Back in the day, when staggered pole-pieces were conceived, the 3rd (G) string on a guitar was wound. It was a weedy little wimp and had the lowest output of all six strings. So the guys at Fender popped a super-tall pole piece underneath it. All was well with the world.
Until guitarists decided they liked bending strings and string sets with unwound 3rd strings because common. An unwound G-string has a crap-ton of output compared to it's wound brother and that tall pole piece grabbed even more of that and shoved it out the amplifier.
The result is that pickups with a vintage-correct stagger can now have an overbearing G-string.
What's to be done?
Well, you could swap the pickups for ones with unstaggered—flat—pole pieces. This runs the risk of butting up against the original problem of the pickup not matching the radius and sensing lower output on the middle strings (although, in practical terms, it's not really that much of a problem).
You could go with one of the modified, modern, staggers available on some pickups (e.g. Kinmans).
Or—and here's the funny thing—you could do nothing.
Oddly, enough, this issue doesn't bother many people. I've spent enough time trying to balance string-to string output that, when setting up a guitar, it drives me nuts to hear that overbearing G-string next to a wimpy D. Thing is though, most people don't notice when playing or listening to a solo guitar and almost no one (myself included) will notice when it's in a mix.
Certainly, the people in the front row—or the guy rushing to the toilets at the back of your stadium gig—are unlikely to wonder why the G is too loud in the mix.
If this really, really bothers you, you'll probably need to consider alternative pickups. If it's just niggling you a little, I'd say, live with it—probably nobody else cares. And, if you hadn't noticed until I started talking about it, I'm sorry. ;-)
Left or Right?
Spare a thought for the poor southpaw, by the way. Our left-handed brothers and sisters don't just have a hard time opening tin cans, they need to consider pickup stagger if replacing pickups in their leftie axes. As standard, stagger assumes you're strung up right-handed. If you want to be vintage-correct, you'll need to find a left-handed stagger. Lots of pickup manufacturers make 'em.
Swapping staggered for flat (or vice-versa) might give you a slight tonal shift. Again, it's quite possible that you'll be the only one that notices it if it occurs but it's something to bear in mind.
Obviously, if you have adjustable pole pieces—or adjustable pickups like the P-Bass—you don't need to worry. You can just listen carefully and smugly tweak the pickups according to what your ears tell you.