We allow it, but there's a few limiting factors going on:
First and foremost, arcane magic is Evil in my world. Only evil races use it, and no good has ever come of it historically. "The Cerulean wastes, well that's what happens when arcane rituals go bad, son". So anyone with a reasonably good power perception skill knows the party is evil. Even without that, if _everything_ the PC's own is magical, anyone with a decent power perception is either going to think they're a lot more capable than they are, "Come help us with the rampaging dragons" or is going to think they're rich and perhaps need to be relieved of some of that wealth.
Secondly, it just takes time. If the arcanist only uses the first 25 percent of their power points, a mid-level caster can embed maybe one or two spells at a time. If the arcanist uses all their power points there's two problems. One they stand a significant chance of fumbling, and arcane fumbles are much nastier than standard ones. Make the arcanist read and reread that table. Secondly, if they cast into penalties, they're at penalties and low on power if anything happens while they're sleeping/resting. A few night time encounters with the arcanist at -30 due to power points will encourage discipline.
Second and a halfly, most parties can burn through a lot of runes in a single encounter. For sake of example, lets say a 4 person party, each burning two +20's and six +10's on weapons, two +20's and six +10's on armor, a blur, a shield, a leap and two heals. That's 4*(10+12+10+12+5+9+5+10) or 292 power points in a single fight. So long as the party has more than an encounter every week or so, the arcanist is likely not going to have the power points to keep the party covered in level 2 and 3 spells.
Thirdly, they're not as good at attacks as people think. The way we play it, any runed spell is cast at it's level, not the casters level. Also, any attack occurs with 0 skill . . . the spell itself is not skilled in 'directed spells'. So a sleep spell cast by the caster attacks with +10-20 on the BAR table, and then the victim saves against the casters level. Cast out of a rune it attacks with +0 on the BAR table and the victim is resisting against a level 1 spell. Generally after a few failed attempts at attacks the PC's have favoured utility and defensive spells. "Why did i just spend a 75 percent action casting a 0 OB shock bolt?" Even then the duration of those spells is very low as they're duration is determined by spell level, not caster level. A 1 minute duration blur is nice, but when you can cast it for 1 PP and it lasts 5 minutes . . . it's not as cool.
We've currently got two campaigns with parties with arcanists in them. The biggest issue that's cropped up has been the inordinate amount of EP the arcanist earns while 'spell-whoring'. To that end we came up with a new category of spell ep, for 'very routine spells'. Spells cast routinely (I cast warm solid on my bed every night) that do not require manuver rolls earn no EP, but require no failure roll. It saves time, keeps the arcane caster from outstripping the fighter for EP's and further encourages only doing bladerunes through those first 25 percent of power points. Before we implemented this, the arcanist was making a little more than twice the ep of everyone else in the party. Although . . . my arcanist does rock