Salutations,
I will give it a shot.
Statistics:
D20M- Uses hit points, and has a massive damage check at DC = Con
Spycraft- Use VP/WP, crits do damage to WP
Races:
Both allow only human, but both offer a different way to differentiate characters.
D20M- Occupations(each offers different bonuses)
Spycraft- Departments(each offers different bonuses) of training
My opinion- departments are well balanced and in further books have shown they can represent past vocations. D20M's occupations seems to have no system to them and are not very balanced at all.
Classes:
D20M- 6 base classes that each revolves around a stat (STR, CON, etc)
They go up to 10th lvl and each offers bonus feats and talents. Talents are class abilities, but can be chosen. So your strong hero can take a talent that allows him to do more melee damage or a talent that allows them to carry more.
It is expected you will go into an advanced class- which is a step between a base class and a prestige class. Some examples are: soldier, martial artists, daredevil. They give more specific abilities.
Spycraft- 6 base classes that each revolve around a spy stereotype (soldier, faceman, wheelman, snoop, fixer, pointman).
Each class goes to 20th level and they range in flexibility, but none as flexible as the D20M base classes. High level abilities of classes are very powerful.
My opinion- I think the D20M classes are generally too weak and the generic base classes turn me away.
Skills:
D20M- Ported from D20, but added more skills for modern use. Some skills are better explained.
Spycraft- Ported from D20, but added more skills for modern use. Added a critical success/failure system to skills.
Feats:
D20M- Ported from D20, but added more skills for guns and many +2/+2 skill feats.
Spycraft- Many are ported over, but a lot more added. There are many mid and high level feats. There feats are broken into types: chase, skill, melee combat, ranged combat, unarmed combat, gear, and style. Some classes/departments give bonus feats restricted to a type, but generally feats can be taken from anywhere.
My opinion- There are way too many +2/+2 skill bonus feats in D20M. I think it is time that these feats are just made into one general one.
Spycraft feats give some high level ones- which is much needed. There are way too few high level feats, especially combat-related, in standard D20. The skill feats give more some more options on customizing skill lists and even just getting more skill points.
Equipment:
D20M- PC gets a wealth rating which they check against to purchase something. It represents the abstract nature of credit and such.
Spycraft- PC gets budget/gadget points to buy standard gear for their character, and they missions points to buy specific gear for the outlined mission.
Armor:
D20M- Makes you harder to hit
Spycraft- Reduces damage (most of the time)
Combat:
D20M- With guns doing 2d# damage and the D20M burst feat, it can be very deadly. The massive damage check comes up often.
Spycraft- Breaks villians into three categories: minions, henchmen, and masterminds. Only the latter two can crit against PC. It can still be very deadly.
My opinion- players will learn to use cover in either system or will make a lot of characters
Chases:
D20M- Very strategic. It is basically d20 combat with cars. The GM needs to map out the area and consider a lot of possibilities.
Spycraft- Very cinematic. The drivers choose manuveurs (depending on who is predator and who is prey) and make a contested skill check to see who succedes. No mapping required, and many manuveurs will change the nature of the race (short cuts and such). The downside is the system gets a bit harded to handle when there are more then two vehicles, but it can be done.
Action:
D20M- Gives action points to pc (number determined by class and level). They can be used to alter rolls and activate class abilities. They refresh when pc levels.
Spycraft- Gives action dice (the die type determined by level). They can be used to alter rolls, activate criticals, and activate class abilities. They refresh each session of play.
My opinion- If you believe in slow level'ng (as I do), then the refresh system of D20M is a killer considering it is used for class abilities.
Magic/Psi:
Both are in the base D20M book, but you will need to buy Shadowforce Archer for the Spycraft rules.
Magic:
D20M- same as D20, but only available in advanced classes. So at 5th level you learn your 1st level spell.
Spycraft- Magic is largely classless. You gain access by feats and use followers/worshippers to cast spells. There are few minor spells, but this is mostly a npc-based system.
Psi:
D20M- same as D20, but only available in advanced classes. So at 5th level you learn your 1st level ability.
Spycraft- Base classes(iirc) for psi, but the system is largely skill/feat related. Many of the powers are similar to standard d20 system, but the mechanics are changed.
Support:
D20M- There are a lot of companies that will be coming out with a range of different books. It also has Polyhderon to give montly ideas.
Spycraft- Mostly AEG, but there is at least one other company producing books (eventually) for the game. AEG seems open to others doing the same, but wants control over who is producing what under the name of Spycraft.
I hope that helps a bit.
Or, at the very least, say that minion crits would deal double Vit damage. 
