lpdeluxe said:
Fret wear shouldn't change intonation. These days, it's really unlikely you'll get a factory made guitar with bad fret-to-fret intonation, although bridge-to-fret, being adjustable, can get out of whack and should be checked, especially if you have changed string gauges.
That said, I'll bet it's worn strings. they get stretched out and don't bounce back when they are tuned & played.
Fret wear can have a huge effect on intonation. What happens is that, as the fret flattens out (which is what happens sometimes) the contact point moves a little further from the bridge, making it play a little flat. It seems like a little change, but it can make a big difference. If the fret wear is uneven (as it almost always is), then you can have some serious intonation problems.
It could also be old strings, which cause real headaches for intonation, or it could be the neck moving due to climate changes. You might, possibly, have a bad set of strings (or, if you have changed the strings, you might have had two. It happens.)
If your nut is not adjusted right, it will cause the first few frets to be high, as the string is being stretched more in those positions than in higher positions. This is an almost universal problem on guitars with factory setups. They just don't do it right (for good reason, as their primary concern is that the guitars never buzz, no matter who is playing it).
You could, possibly, have too much bow in the neck. This changes the contact points on the strings. Fret locations are measured in thousandths of an inch, so any minor change in the geometry can have an effect.
What you need to do is take your guitar to a good repair shop. If you don't know who is good in the area, ask around. The professional musicians know who gives them what they need. You will pay more than you might from someone else, but you get what you pay for with a setup. It is not as simple as many would make it out. They will be able to tell you if it is just a setup issue, or if you have enough fret wear that some fret work is in order.
It sounds to me, though I can't say for sure with out seeing it, like you need fret work, but probably just a fret dress. Basically, a fret dress involves leveling all the frets until they are all the same level, then recrowning them (or making them all round again). This is a VERY high skill job. Don't even think about doing it yourself. You will not be happy with the results. We charge $125.00 for a fret dress, so you can probably expect to get it done for some where between $110-$165. If it is less, then be concerned about their qualifications. You want a PROFESSIONAL, not a hack.
You may need a refret. This is considerably more expensive ($300-500 in my shop, depending on a variety of other issues), so one hopes a dress is enough. You may even be able to get by with just a set up ($75-110 for an electric in my shop).
If you need fret work, it may just be that you are one of these guys whose style is hard on frets. That does not necessarily mean you play hard, just that what you do is hard on frets. It kind of sucks, but it is not uncommon. I have customers who need refrets every year. Now, it is not usually a case were they wear out their frets completely in a year. It is simply that they prefer the fell of taller frets. Most people can't tell the difference between a dressed fret and a new fret. Some people can. For those who can, we now have a new option: Stainless steel frets. They suck to work with, but they are MUCH harder than traditional nickel-silver frets (which have no silver in them, BTW). Because of this, they last a lot longer. There are only a limited number of sizes available in stainless, but they are popular sizes. Stainless can, according to some, make a guitar a bit brighter, but I have not noticed this, myself.
If you are showing major fret wear after three years, you might want to consider stainless. We have an additional up charge of $150 for stainless, because it is so hard to work with, but they should last you quite a lot longer, so the value is there.
Light
"Cowards can never be moral."
M.K. Gandhi
When I told him he needed new strings he said......"you mean you have to actually CHANGE strings?" 
Go figure.
