I don't have the sourcebook in front of me, but looking at the online d20pfsrd here, Finesse Rogue is a basic level Rogue Talent, which become available for taking at 2nd level. The 'Feat' Rogue Talent is listed as an 'Advanced Talent', which isn't available until 10th level. So when a rogue is 10th level, yes, the 'Feat' talent makes the 'Finesse Rogue' talent redundant. But before 10th level that isn't the case.
Yes, there is a good reason for feat prerequisites.
Two reasons, in fact:
To clarify by indicating what build a feat is intended for (a feat that boosts Lay on Hands usually requires that you have Lay on Hands)
To balance by forcing players to dedicate more resources in order to take a more powerful feat.
I suspect the reason you're surprised to encounter this is that by and large 4e feat prerequisites are for clarity: if there's a feat we want, we probably already qualify for it. (In previous editions of D&D prerequisites were much harsher and it was common to plan our characters around qualifying for certain feats.) It's surprising to find a feat we want that we can't take in 4e.
Mastery feats need to be balanced carefully:
Feats like the Mastery set can be very powerful: they double crit range from 1/20 to 1/10, and for a build that 'fishes' for critical hits that's pretty massive (other builds wouldn't be as impressed by it, but a feat's value shouldn't be based on its usefulness to a character that wouldn't take it anyway). Consider a burst/blast wizard who attacks an average of 4 targets each round: compared to a character with expanded crit who makes one attack in the same time, the wizard with expanded crit will deal maximum damage every 3 rounds instead of every 10. If he has specialized in making his criticals awesome, this is very powerful.
In order to allow such feats to exist without unbalancing the system 4e has imposed more stringent prerequisites to take them. But...
The requirements really aren't that harsh:
Prerequisite: 21st level, Dex 15, Int 21, Wis 15, wizard
At level 21 two of a character's abilities can have increased by +6, and the other four abilities have increased by +2. This means that for Wizard Implement Expertise I can start with (before racial modifiers, assuming I take a race with +Int) a 13 Int, Dex, and Wis to qualify at 21 without focusing on either of those secondary stats or having racial bonuses to them. Roughly two out of every three wizards will have focused on at least one of them, and it's important to remember that the 4e stat generating system makes it impossible for me to start with less than a 14 in at least one stat.
A player who wants the feat should have been considering it ahead of time and planned accordingly--but even a wizard who hadn't planned to get the feat is likely to qualify. (If I want it so bad anyway, I've got two +1 stat bumps at 24 and 28 to bring my 11 up to a 13 and still enjoy the feat for the last three levels of the game.)
Sure, change it if you like.
The phrase "feat tax" gets thrown around a lot. It seems to mean that there are specific feats I need to take in order to not be a burden on my party. I generally disagree with this idea because it presupposes a specific kind of character optimization which is just one style of play rather than a philosophy of the game design.
Feat slots are limited for a reason: to force choice. There are better and worse choices, though 4e has done a surprisingly good job of limiting downright awful choices. By lifting feat prereqs and granting free feats, your group would be saying these choices aren't part of the kind of game they want to play.
And if that's your party's play style, go for it: there's no wrong way to play the game provided everyone's safe and happy. But it's not the way the game was designed, and the game wasn't designed by accident (however much I joke about the adventure writers), so we're less surprised by mechanics like these if we understand the original philosophy behind them.
Best Answer
Officially, you have the feat twice and they do not stack
You cannot generally select a feat that you already have, but if you are granted a feat you already have, you end up with two. Unless the feat has a Special section saying that it stacks with itself, it does not. Weapon Finesse does not say this, so the two copies of Weapon Finesse are redundant.
Player’s Handbook II has retraining rules
The Player’s Handbook II has retaining rules you can use to replace the Weapon Finesse you originally selected (not the one from swashbuckler, as you had no choice in that one). This can be quite expensive and time-consuming, depending on how long ago you made this choice, and you will need your DM’s support to use it.
Expanded Psionics Handbook has psychic reformation
Psychic reformation allows far quicker and cheaper retraining than PHB2’s retraining rules, but you have to find a 7th-level psion or wilder who knows it in order to use it. If you do, hiring him or her to manifest the power will cost you a minimum of 530 gp. Alternatively, a power stone of psychic reformation costs a minimum of 950 gp. That can be activated by any psion or wilder (with a relatively easy manifester check if they are below 7th level), or anyone who can make a DC 24 Use Psionic Device check.
In both cases, the service or the stone will cost an additional 250 gp times how many levels ago you selected Weapon Finesse the first time. For example, if you are level 5 and chose Weapon Finesse at 3rd level, the service will cost 1,030 gp, and the stone will cost 1,450 gp.
Again, this cannot replace the Weapon Finesse from swashbuckler; it only lets you remake choices you made in the past.
Fiendish Codex I: Hordes of the Abyss has the DCFS
Embrace the dark chaos replaces any feat you have (e.g. including that Weapon Finesse from swashbuckler, or even more ridiculous things like the weapon proficiency feats from the elf race) with an Abyssal heritor feat.
Shun the dark chaos allows you to replace any Abyssal heritor feat you have with any other feat you qualify for.
So you can embrace the dark chaos and then shun the dark chaos to swap any feat for any other feat. This is a broken, theoretical-optimization trick known as the Dark Chaos Feat Shuffle, or DCFS for short, and is not recommended in a real game. In any event, both are 8th-level spells that cost 250 XP, so quite expensive compared to psychic reformation (but far more flexible).
Many tables houserule this situation
In my experience, it is extremely common to insert the words “If you already have [feat you would gain as a bonus feat], gain any other feat you qualify for instead.” The only official use of this sort of thing to my knowledge is the marshal from Miniatures Handbook, but it’s a good idea that eases headaches and somewhat reduces the need to metagame-plan your character out ahead of time.
I strongly recommend you ask your DM for this option. It’s fair, and improves the game.