I don't think Wizard 6/Cleric 6 or Cleric 6/Druid 6 is the problem with that house rule. The problem is something like Cleric 1/Druid 1/Sorcerer 1/Bard 1/Wizard 1 at level 5. It's very MAD (which may be enough to balance it!), but assuming a 14 in all 3 casting stats, you'd be able to prep 3 cleric, 3 druid, and 3 wizard spells, choosing the best from levels 1-3 of each list, as well as knowing 4 bard spells and 2 sorcerer spells (assuming you wait until level 3 and 4 to take them, so you can choose 2nd level spells.)
You know, even considering all that, I don't know if it's THAT bad. I think it depends on how much you value spell diversity. I would say a mid-level caster grabbing level 1 dips to expand their spell list broadly is the biggest possible breaking point. That and a Paladin 2/Sorcerer X getting to access the powerful mid-level paladin spells at the cost of 2 sorcerer points and 1 caster level.
A solution for the single level dipping might be:
PCs effectively get spell points based on level. So, a Cleric 11 / Wizard 1 would get 89% of total spell points for Cleric spells and 9% of spell points for Wizard spells. The rest of the spell prep / slot / cast are basically the same, but the PC could cast a few higher than first level Wizard spells per day.
For example, 12th level full casters have 47 "spell points" (i.e. multiply level of spell slots by number of each level slots and total, remainder goes to highest level class or whatever).
So, a level 6 Cleric / 6 Wizard would get:
1st 4 2nd 3 3rd 3 4th 3 5th 2 6th 1: Cleric 24 SP, Wizard 23 SP (just like always, but there are these 2 additional spell point numbers on the character sheet that have to be kept track of)
The PC casts a 4th level Cleric spell:
1st 4 2nd 3 3rd 3 4th 2 5th 2 6th 1: Cleric 20 SP, Wizard 23 SP
The PC casts a 5th level Cleric spell:
1st 4 2nd 3 3rd 3 4th 2 5th 1 6th 1: Cleric 15 SP, Wizard 23 SP
The PC casts 3 3rd level Cleric spells:
1st 4 2nd 3 3rd 0 4th 2 5th 1 6th 1: Cleric 6 SP, Wizard 23 SP
The PC is running out of clerical spells he can now cast. If he casts the 6th level spell (or 3 second level spells) as a Clerical spell, all of the other spells cast must be Wizard spells.
So, a level 11 Cleric / 1 Wizard would get:
1st 4 2nd 3 3rd 3 4th 3 5th 2 6th 1: Cleric 43 SP, Wizard 4 SP
This PC could cast a single 4th level Wizard spell (which he would have had to learn somehow), or a 1st and a 3rd, or 2 second or 4 first. He gains a little bit, but a single dip in Wizard does very little.
Although it is a little bit more bookkeeping, it does give a reason to single dip into a spell casting class (casting a single 4th level spell of a different class per day is nice), and it gives an incentive for someone to go Cleric 6 / Wizard 6 which the core multiclassing rules totally discourages. It still has MAD issues, ASI issues, and other limitations.
The spell points are easy to figure out from level to level. At level 13, the PC gains 1 7th level spell, so the Cleric 7 / Wizard 6 has 54 spell points, 29 and 25 respectively. The PC has ALL of these options of spells to cast, but is limited to about 54% Cleric spells and 46% Wizard spells (more or less).
The Cleric 6 / Wizard 6 PC is super versatile in encounter one, but in encounter four, things might start getting a bit tight and there is no way for him to cast two Fireballs per encounter for 4 straight encounters like he could if he were Wizard 12. He is limited to 6 Fireballs a day, whereas the level 12 Wizard could cast 9 Fireballs a day.
This forces a balance of spell casting between the two classes (even if one of them is a 1 level dip), effectively reducing the number of spells of each class that can be cast per day.
This could even result in a PC having only a 4th level slot available at the end of the day, but he has Cleric SP 2 and Wizard SP 2 available. That's one of the prices of multiclassing. You gain a lot, but there are also limitations and reasons why players would still want to play a full level Wizard (although Cleric 1 / Wizard 11 for AC would probably be more prevalent).