Also, I've already stated how I run it in my games, and it's not how you describe it, the way I run it has been working for me and is very very balanced and fair according to my players, a few of which are math geeks, so I'm not too worried about house rules. However, I would have to disagree with your assertion that the rule is written as it is to make the game balanced, mainly because it is actually rather unbalanced as written - in the favor of the defender. Well, that's my opinion anyway, I guess we'll (hopefully) see when the errata comes out (one day)...
Okay, re-found and re-read*, your table basically turns touch-indirect spells into touch-direct spells that get armor as an added bonus. More streamlined & efficient. I can work with that as a house rule.
And yes, this is one where I would like to see an errata to at least clarify their intent.
I have to agree that, as written, touch spells favor the defender. Intentionally. After all, that's why you get -2 Drain modifier with a touch spell. It's weaker (read, unbalanced, in favor of the defender) than a regular LOS spell, and you suffer less drain as a result. This is due to adding an extra die-roll to establish a mystical link before you do anything else with your spell, if you then streamline the spell, you likewise make the spell simpler (read, pushing the balance back to the caster). It
should be harder to hit with a melee spell and it
should deal less damage than an equivalent ranged spell. That's kind of the point.
All that being said, if your house rule works well for your table in keeping the game moving and everyone has fun, awesome, that's the point of this whole mess. I'm just looking at it from a RAW perspective. Who knows, once I have to go through the actual work of casting a touch indirect combat spell, I might implement the same house rule. As it stands, everyone at my table has access to several colors of dice (by borrowing from my horde, if necessary), so they can say "blue, touch test, red spellcasting", and roll a bunch of dice at once into the felt die-roller thingy (always a must, and that is definitely its official name). Makes it a lot easier for resolving the occasions where you have to roll 2 or 3 pools just to determine the results of a single action.
*How voydangel runs touch-spells:
In my groups we run it in 2 steps as well, but slightly differently than FJs 2 steps.
We go:
1) Establish Magical Link: Standard melee combat test. (Unarmed Combat + Agility vs Defense test) The attacker/caster gets +2 dice because only a touch is required as per SR4A pg. 159.
2) If the melee touch attack succeeds: Spellcasting + Magic vs. Body/Willpower + Counter-spelling (and some armor and other random stuff if applicable to the spell). To determine spell effectiveness/potency.
This is fairly directly explained on pg. 183 where in Step 3: "Choosing a target", it mentions that if its a touch spell you must succeed in a melee attack vs the target to create the link. Then in step 4 you make your casting test, then step 5 the target resists.
Also on pg 203, it explains that a standard melee attack is required as part of the complex action of casting when using touch based spells.