It might break things a little. For example, each hero is its own unit, so is disproportionately valuable as an initiative-stacker in a by-unit system. But basically the way to do it would be to drop the Command points altogether, as well as anything else that nets you a "command" card.

If I were you I'd try the Initiative as written. It makes tracking the turn to completion easier and keeps an element of doubt. It also makes the game quite chaotic (which I like).

I didn't say it was pretty. I said it was awesome. Well OK the spaceships are pretty AND awesome.

Vit C, Zinc, and if you get coldsores, a high rate of L-Lysine. Keep the fluids up.

Cool! If you get it all typed up, you could ask TNJRP about hosting the file so we can all have a look at it!

Anyway, I hope I'm being helpful. If I'm spewing junk data just slap me.

I'll start with the Commander questions, since they're the easiest.

#2
In a non-matrix army, such as Orks, there is 1 overall Commander/Leader. In this case he's called a Big Boss. My plans for him are to create a unit with him as the only member and make him a level 1 or 2 commander. This will gain me an extra activation card(s). If another one of my units has several broken figures, can he join that unit to help with individual rally rolls? This would mean 2 units have now joined together.

A Primary Commander IIRC must be chosen as part of a standard unit, ref page 14 "How Units Activate" subheading "Primary Commader". HOWEVER he can leave that unit the start of any turn, and freely join another unit at the start of any subsequent turn: ref page 19, "Commanders" for more details. In other words just roll with the standard rules on this, they're quite close to what you want.

EDIT: I'm pretty sure you can legally create a standard unit that is just the commander. That uses up one of your 15 Standard Units. But, you really don't need to. But, I wouldn't object to an opponent doing that, anyway.

#3
Continuing with the above situation. Say the commander is allowed to join another unit. When would the combined unit activate? When the commander's unit card is drawn or the other unit's card?

When the Primary Commander joins a unit, they use the same activation card- remove the Commander's Activation (not Command) card from the deck. When he splits from a unit, they go onto separate cards again, so put the Commander's Activation card back in the initiative deck.

On to the Matrix questions:

#1
The Games Workshop 40K Tyranid army is a great fit for a Matrix style army. The basic troopers (Termagaunts, Hormagaunts, Gargoyles) are all matrix units. The Tyranid warriors and the Hive Tyrant are Focal Leaders. My question is, how do I assign Tyranid warriors to lead Termagaunts? I think the answer is to create Ad-Hoc units. For example, combine a unit of 10 Termagaunts with another unit of 2 Tyranid warriors both of whom are Focal Leaders. Is this correct?

While correct it may be sub-optimal. If this helps, a Focal point is not necessarily a Leader, it just indicates that the group intelligence networks through a particular node. I'd just allow Focal Points in any Matrix unit; it could mean that the Hive Mind happens to be focusing some attention on that swarm at this moment.

Otherwise, yes, Ad-Hoc or mixed-frame and therefor Exclusive units would be the go IMO.

In Reaper's game, Warlord, which has a slightly similar initiative system to Defiance, taking too few units (and hence getting too few initiative cards) is considered a significant error. In that system, individual heroes (called Solos) are used to pad out the deck. In Defiance the idea is not to go first, or last, but to manipulate initiative so that your opponent is always reacting to you and conversely to be able to react quickly yourself if your opponent gains the upper hand; to have more cards in the deck increases uncertainty for HIM while offering finer granularity in tactical decisions for YOU.

Damn, this is hard to express clearly. It's subtle in concept but can be violently and lethally obvious in (make believe) combat.

Flexibility doesn't SOUND important, but try fielding the Devastating Marines from the Black Watch (and Demian's Star Marines I think, originally). The simple fact of two solid, single task, long range weapons falling into Primary and Support roles makes for a unit with no serious, exploitable weakness in a toe-to-toe fight (I refer to Heavy Riveter Pri., Laser Cannon Supp.) Scary bastards.

Let us know how it goes! Watch out for initiative, having that big unit go dead last on the first turn with IF in play could really sting.

In hell.

5% + seems a little harsh for a relatively small forum.

So far I haven't been able to find any specific post -at all- using the search function, due to this rule. Can the filtering be turned off?

Those machine troops tore people a variety of novel new orifices, too. Chief amongst their weapons (apart from surprise and a near-fanatical loyalty to the Pope) was the Dreadbot, a 6J AR something-or-other 2 DC vehicle with an artillery rocket and a backup rack of RoF 4 AV missiles. Apart from that they had a nice range of simple but brutal weapons that really tended to f* people up.

Next time I think I'd like to see them and the Black Watch go toe-to-toe.