Ultimate magus (Complete Mage and also online here) can advance both wizard and assassin spellcasting, as it requires both arcane spellcasting prepared from a spellbook, à la wizard (or wu jen), and spontaneous arcane spellcasting, which the assassin has by virtue of the fact that, “An assassin casts spells just as a bard does.”
You need at least 2nd-level spells on the prepared side and at least 1st-level spells on the spontaneous, so a 3rd-level wizard/1st-level assassin has the requisite spells (though you'll need more levels because of skill requirements of both assassin and ultimate magus).
The ultimate magus advances both classes on 7/10 levels, and only one class on the other three levels (at 1st, 4th, and 7th). In each case, the class that is advanced is the one with the lower caster level. Since wizard spellcasting is better than assassin spellcasting, it is probably best to try to boost your assassin caster level above your wizard caster level, so you can benefit from full spellcasting progression for your wizard side. Practiced Spellcaster (Complete Arcane) helps a lot with this, but ends up being not enough without additionally possessing the krau sigil.
Ideal Case: Illumian 5th-level wizard/1st-level assassin/10th-level ultimate magus
You want to enter the prestige class ASAP, you want to do it with minimal loss of wizard spellcasting, and you want to advance wizard spellcasting at every ultimate magus level, particularly since you’ll already have the highest-level assassin spells even if you miss three like that.
First, you’ll need Hide and Move Silently as class skills, at least for your wizard levels and ideally for the ultimate magus levels as well. You may also want Disguise in-class, but it’s not a big deal since it caps at 4 ranks required, which you can do cross-class if necessary.
Move Silently is annoyingly difficult; Flexible Mind from Dragon vol. 326 is the only good way to get it as a class skill. Barring that, you could be a viletooth lizardfolk (Dragon Magic) but with LA +1 it might be better to just dip something (though having it be always a class skill is useful). Alternatively, an elf (preferably gray elf or fire elf for the Intellignce bonus) could take Aereni Focus (Move Silently) from Player’s Guide to Eberron to get it always in-class as well as a +3 bonus to it (also counts as Skill Focus if that matters to you).
Hide has two easy options, at least: Unearthed Arcana wizard variants can get it for you at level one, at the low cost of your Scribe Scroll feat. You could either take a Fighter feat, and use it for Martial Study (any Shadow Hand maneuver), or if you are an illusionist, you could take the shadow shaper ACF to just get it directly (and add your Int to Hide at 5th level, which is pretty cool). I prefer the Martial Study route as it sets you up for Assassin’s Stance and also gets Hide in-class for ultimate magus levels. Martial Study and Stance are from Tome of Battle.
I will note that I find the lack of a feat that grants both skills in-class kind of strange; they’re certainly thematically linked and plenty of feats do that sort of thing. An Apprentice feat could reasonably combine the two (Apprentice [ninja] maybe? Hell, Apprentice [assassin]), but none of the examples from Player’s Handbook II actually does so.
If you want Disguise in-class, City Slicker from Races of Destiny is a pretty easy choice. Silverbrow Humans (Dragon Magic) also get it.
Anyway, have 8 ranks in Hide, Move Silently, and Spellcraft by wizard 5th, along with the 4 ranks you need in Disguise and Knowledge (arcana). This requires at least 5 skills points per level (4 if you have Disguise in-class), but even with 2+Int skill points a Wizard should have at least 6, particularly a gray elf who gets an Int boost. Which is good because of course you also want Concentration.
Then at 6th level, take assassin 1st and Practiced Spellcaster [assassin] from Complete Arcane to boost your assassin caster level to 5th, matching your wizard caster level. At 7th, it’s your 1st level of ultimate magus, and your caster levels between wizard and assassin are equal, so you can advance wizard. At this point, you have a choice. You could leave well enough alone, accept that you’ll miss a second Wizard level at ultimate magus 4th, and thereby gain 9th-level assassin spellcasting instead of 8th-level.
Or you could be an illumian with the krau sigil, which provides a +2 caster level bonus quite similar to Practiced Spellcaster.
So my conclusion is an illumian 5th-level wizard/1st-level assassin/10th-level ultimate magus, with 15th-level wizard spellcasting and 8th-level assassin spellcasting.
For basics, Beguiler 1/Wizard 4/Ultimate Magus 10 (or however far you get) is by-far the best choice. Beguiler 2/Wizard 3 as entry is not going to get you killed or anything, but it is a dramatic loss of power relative to only a single lost wizard level.
Cloaked Casting
From an optimization perspective, Cloaked Casting isn’t nearly worth what you lose in terms of wizard spellcasting.
Unfortunately, Cloaked Casting is rather minor in general. There’s no reason you can’t surprise your opponents with your spells, and just not get the +1 DC bonus. Surprising people is usually a pretty good idea anyway (though feinting in combat is not). You will be better off doing things this way.
But feel free if you really want Cloaked Casting to get it. Just be aware that it will cost you more than it ought to.
You don’t have to ban Illusion if you don’t want to
Wizards get illusions that beguilers don’t, and your wizard spellcasting will be superior to your beguiler spellcasting. If illusions are important to you, keep it on your wizard; having it on both classes will really play up its importance to your character.
So illusion could be very valuable to you; don’t ban it just because you think it will be redundant. It won’t be if you use it right.
You really don’t need area-damage
Conjuration and illusion are excellent at battlefield control, which means rather than simply damaging people in areas, you’re hitting people in areas with nastier effects, and stuff that warriors cannot do. Damage is easy, and lots of classes do it as well, if not better, than spellcasters. In a lot of cases, though, that’s all they can do. So let them do it.
And ban evocation.
Metamagic
Go for it! Ultimate magus gives you powerful abilities that allow you to use your second class to power metamagic for the first, which works very well. Definitely a good choice.
Shadow Spells
Ideally, you do not want to use shadow evocation or shadow conjuration offensively, because you give the enemy two chances to save, which is bad. As such, I don’t really suggest relying on them for that; they’re massively better as buffs or what have you. Spell Focus (Illusion) is still a solid idea though.
Best Answer
In the new Hybrid Classes in Pathfinder, the Arcanist is closest to what you're looking for. I don't think the mechanics are one-to-one between the Ultimate Magus and the Arcanist, but the core idea is the same.
Hybrid Classes are meant to combine the ideas of two different classes into a single working class, and so the Arcanist combines the prepared and spontaneous spellcasting of the Sorcerer and Wizard, adding some interesting interactions and class abilities.