A good post, O'Etaipos, and I agree with much of what you say. But there are two reasons why we occupy different positions on the significance of Issus and Gaugamela.

1. We disagree on the factual inferences that we believe ought to be drawn from the sources.

This is partially because I'm highly sceptical of those sources, and believe they ought to be treated like a biography of Simon Bolivar authored by Hugo Chavez. Interesting yes, full of facts, probably, but unquestionably biased.

For example, I'm not sure why you feel so confident in stating that Darius was completely discredited after Gaugamela, and that he had lost control of the empire. The Chaldaean tablets pass this judgment on Gaugamela:

The king, his troops deserted him and to their cities they went. They fled to the east.
I suggest that these tablets, in saying that the troops deserted the king, could well be referring to Bessus and his premature retreat (which, after all, lost the battle for the Persians - is it so unreasonable that they perceived this fact for themselves?). If the Persians laid the blame for Gaugamela with the unreliable Bessus, then Darius' reputation might have been intact at that time. In fact, Bessus might have committed his treachery out of self preservation. This is not the standard interpretation, but nor is it a far-fetched one.

The idea that Darius was discredited and powerless is promoted by Arrian, who describes a poor lost soul hanging out at Ecbatana with nary a soldier to defend him. But Arrian, for all his merits, wrote centuries after the event and was not without his biases. By contrast, the astronomical records of the Chaldaeans were contemporary and intended to be scrupulously accurate.

Other Hellenic sources conflict with Arrian's account. Plutarch tells us that a number of Persians defected to Alexander after the betrayal, apparently out of a sense of disgust. This doesn't sound like something that would happen if Darius was as isolated as Arrian suggests he was.

Further, Curtius Rufus states that Darius had assembled an army of 30,000 infantry at Ecbatana (including, for the record, a number of Greek mercenaries), as well as a few thousand cavalry. Not a bad effort for just a few months of work. No doubt there were some Persian subjects who were playing a waiting game to see who would prevail, but (according to Curtius Rufus, anyway) it looks as if there were still plenty of men who were willing to defend the empire. If Darius had not been betrayed, he could conceivably have finished raising another grand army for a third great confrontation with Alexander.

I think you might have also just gotten some things wrong. For example, I don't know why you say that the Spartan offensive was easily beaten. It appears to have lasted from 333/332 BCE to 331/330BCE (at least until after Alexander sent those Athenians home), Agis III enjoyed considerable successes in both Crete and the Peloponnese, and Diodorus of Sicily describes the final battle with Antipater thus:

When it came to a general engagement, Agis was struck down fighting, but the Spartans fought furiously and maintained their position for a long time. When their Greek allies were forced out of position they themselves fell back on Sparta. More than 5,300 of the Spartans and their allies were killed in battle, and 3,500 of Antipater's troops.
That battle was on the same scale as Chaeronea and (according to the description) more fiercely contested. The very fact that the sources generally don't talk about it much should tell us something about how they've all chosen to portray the war with Persia.

2. We disagree in our conjectural attempts to fill in the blanks.

There were counter-attacks after Issus. We have very little information about them at all, although what information we do have suggests that they weren't small-scale affairs (see eg Agis III).

I suggest that the very fact they were initiated at all suggests that they had a decent chance of success. Darius wasn't exactly a wild risk taker. Memnon was sent to fight a defensive war against Alexander in Asia Minor, not an offensive one. At both Issus and Gaugamela, Darius assembled large forces and moved them about carefully. Why, then, would he throw away the lives of his men in frivolous counter-attacks?

You suggest that Alexander sitting in a siege camp for 7 months indicates that the attacks were not serious. That's not an unreasonable conjecture. But then, what else was he going to do? Retreat to Lydia? To the Peloponnese? That would have been tantamount to an admission of failure in the Persian campaign, and then how loyal would his Greek allies have been? Perhaps more importantly, where's the glory in that?

Alexander had soldiers and commanders scattered throughout his nascent empire. I suggest that he took a (calculated) risk that they'd be able to ward off the Persians (and their Hellenic allies). The fact that he took these risks doesn't mean they weren't serious. Alexander's entire life was full of him taking serious risks, from taming Bucephalus to the assault on the Malli. One wonders if the man had a bit of a problem, actually.

Is it then so far fetched to suppose that, after Issus, he took another great gamble and trusted sub-commanders around the empire to resist the Persian counter-attack?

That's more than enough for one post.

Note: I don't want to get trapped into the position where I'm arguing that the Persians weren't in serious trouble. They were - right from the get go, in fact. I'm arguing for the more limited and reasonable position that Issus and Gaugamela were important events, but that they did not spell the end of the Persian Empire.