The main difference between Alternate Earth and Glorantha is that we have a huge body of literature on Alternate Earth and very little on Glorantha. This means we have an enormous amount of information about the deities of the ancient cultures of Alternate Earth, far more than we have about the deities of Glorantha. This can be both a blessing and a curse. It is a blessing because we need only pick up a book on mythology to read a description of all of the Celtic deities, and another to read the stories of the Irish deities or the Welsh deities. It is a curse because we do not have a blank page to start with, we must follow the stories and legends that already exist.
How, then, do we start filling in the pantheons of Alternate Earth? The easiest way is to split the cultures into discrete Pantheons and then fill out the powers of the deities. I started with the deities of the British Isles as part of my Arthurian Britain idea for Alternate Earth RuneQuest. This involved splitting the Celtic deities into pantheons for Ireland, Wales, Britain, Scotland, Gaul and the Germanic peoples. However, this brought some problems to my attention, for these pantheons were obviously not as discrete as they first appeared. In fact, there are many deities common to the pantheons. How should we approach this problem and how to deal with it?
For instance, the Irish pantheon has Lir and Manannan mac Lir, both gods of the sea, the Welsh pantheon has Llyr and Manawyddan ap Llyr, both sea deities. The Irish have Nuada Silver Hand, the Welsh have Nudd Silver Hand, the Irish have the son god Lugh and the Welsh have the sun god Lleuw. The Irish have a legend of the Golden Apples of the Sun that bestow immortality, as do the Welsh, the Germanic peoples and the Greeks (Apollo went to the far north to find these). What do these similarities mean? Do they mean that the common Indo-European roots of these cultures have been preserved in the myths of the different peoples? Do they mean that the different cultures borrowed myths from the other cultures? Do they mean that these deities were worshipped by the different cultures in different ways? I prefer the last explanation, that each of the different cultures worshipped the same deity in different ways, forgetting some of the myths and only remembering those myths that affected their culture. So, an Irish worshipper of Lugh could regain his magic at a temple to Lleuw in Britain, and a British worshipper of Brigantia could regain her magic at an Irish temple to Brigit.
So, we have a series of deities that are spread across the whole of Europe, these are the original Celtic deities that were worshipped by the proto-celts. These deities include Lir, Manannan, Brigit, Nuada, Bile, Danu, Goibniu and The Primeval Cow. The Greeks knew of the Titans, vast primeval deities who ruled before the time of the Olympians. My personal opinion is that these primeval deities were common to the Greeks, the Celts and to the ancient people of Europe. We also have a number of magical items that are common to the cultures, these include the Golden Apples of the Sun, Cauldrons of Rebirth and Cauldrons of Plenty. For the purposes of Alternate Earth, I will be assuming that these are the same items that have been mentioned in more than one culture.
Where the deities are similar, in my opinion the same, I have used the same spells and skills. Where the deities are similar but different, I have used similar skills. After all, how many spear/shield wielding Celtic wargods do we really need?
As to ensuring that the legends of the cultures are consistent, this is a near impossible task. After all, how can we marry the legends of the Irish and the Greeks? They have different accounts of the origins of the earth and of the gods. However, we can make some assumptions that are practical for Alternate Earth. First, the deities existed and were worshipped in RuneQuest cults. Second, common elements in the mythology reflect shared elements. Third, legends of the origins of people are probably true, for the purposes of Alternate Earth. So, the Milesians did come from Spain and were probably the earliest Celts to reach Ireland. The Fir Bolg came from Thrace and were probably sea-borne settlers. The Britons did invade Ireland, but were forced back. Raiding between Britain and Ireland was common, as was raiding between Britain and Gaul.
As to timelines, it is very difficult to establish timelines for the different accounts. We know that the Milesians are supposed to have come to Ireland some time during the second millennium BC, possibly around the same time as the early Mycenaean Heroic Age. The Tuatha de Danaan came just before this, so would be around the start of the second millennium BC. British accounts are later than this, pointing to a first millennium BC origin, probably as a second wave of Brythonic/Goidelic Celts came across Europe. The later Welsh legends take place either in the last days of the first millennium BC or after the Roman Conquest and even after the Roman Departure. There are several Irish Hero legends that take place in the first, second and third centuries AD. However, for game purposes, this is pretty irrelevant. If your campaign is set in Arthurian Britain/Ireland then what do you care when the mythological events actually happened? However, if your campaign is set in Heroic Age Mycenaean Greece, it may be important if you travel to the islands in the Atlantic - you might meet the Tuatha de Danaan or the Milesian invasion of Ireland, in fact you might take part in the invasion and defeat the Irish Deities.