Again, never seen it happen in my games.
And that doesn't mean the problem doesn't exist. 3.P is called "caster edition" for a very good reason, which I think is relevant to bring up in a topic about Pathfinder problems.
If a dungeon has say twelve locks in it - the wizard with the knock scroll is probably not taking the knock spell ("I have it on a scroll") so that's still only one out of twelve locks. Sure, he gets that lock, but is she really going to have twelve such scrolls? Where does she get the time and money to make them? And does she want to, or would she rather spend her time and money elsewhere.
Knock is a level 2 spell, which is still really cheap to make, and you can throw one in a wand and never need to prepare it again.
I'm not sure that I understand what you mean here. How do you leave a spell blank? Your DM allows you to prepare spells without picking which spells are prepared? That's broken right there and shouldn't be allowed. Or do you mean something else?
http://paizo.com/prd/magic.html
When preparing spells for the day, a wizard can leave some of these spell slots open. Later during that day, he can repeat the preparation process as often as he likes, time and circumstances permitting. During these extra sessions of preparation, the wizard can fill these unused spell slots.
This takes about 15 minutes(reduced to 1 minute with the Fast Study Arcane Discovery).
I have yet to see a game where the wizard always has all the spells they want at exactly the right time. Typically they have enough spells to deal with about 25% or so of the situation, which seems about right to me in a party of 4.
This is why I said they prepare general purpose spells that are useful in a wide variety of situations(like Fly, Color Spray, Sleep, etc), then putting the more situational spells, like Knock, on scrolls and wands.
And the party resting at will is very much a DM problem.
Don't get me wrong, I don't normally prevent resting (I'm a nice guy) but the characters know that anything can attack in the night at any time unless you are in a very safe space.
The party can have other reasons for resting though, like hit points being low, the other spellcasters being out, maybe the Barbarian is out of rages, etc. If the caster rations his spells out, then he would only need to rest during times when anyone else would, which during a night attack is essentially a TPK waiting to happen(though I always try to keep one or 2 spell slots left anyways so I can slap an Alarm spell or something around so we don't get night attacked)
Plus the Wizard is still the last at threat from ambushes since Pathfinder though giving the Wizard an option to be immune to surprise attacks at level 1.
1. Your bards have to use magic for diplomacy? Why? And how is magic more effective than non-magic for diplomacy. This is a game-world/GM problem. Charm is the worst way to make friends and influence people because it eventually wears off.
I never said they do? I said the Bard beating the Wizard out at diplomacy is a bad example because they're both spellcasters.
That said, Bard gets Glibness so they can make friends without charm spells.
2. Invisibility and flight is better than non-magical sneaking (mostly; of course the DM should still be having the character make Fly checks with the result modifying the subsequent stealth check). Until the spell wears off. But rogues can also play this game and turn invisible. But after the spell wears off, they still have the edge.
Unless I really need to egt into somewhere stealthy, the fight should be over by the time invisibility and flight wear off. Even then, I can just stealth in, get what I need to, then teleport/Dimension Door away.
3. The wizard can outdo the fighter in damage for one or two rounds, but not for much more than that. But seeing as how they used some of their best slots for outsneaking the rogue, that's not going to happen today.
2 spell slots was all that was needed to otudo the Rogue. That's hardly crimping my ability to fight for the day, especially when I can just summon a monster to help end the fight with one spell used.
4. Fair enough. But I have seen some people try to make magic be too good by making it always work as desired, which, by the RAW, it does not.
Again, I see people claiming all the time magic doesn't always work if you follow the spellcasting rules, then they never mention what rules they're referring to.