Siding with the Alliance in a tough fight in the initial stages.
I can speak on NUNS and GE. For starters....
Empire has millions of ships ranging from Super Star Destroyers to the lowly Gozanti-class Cruisers. Hard numbers wise I know sources of follows.
A decent fleet to be honest. For Nuns, its harder to pin point but what is known there is this much. We know NUNS has dozen colonization fleets, and while each fleet is different in exact numbers and make ups, we have some idea of roughly the basic make up and numbers from Macross 7.
The only colonization fleet size we get for Macross fleets with solid numbers is the size of Macross 7 fleet. Used as the standard for sizes. This fleet had nearly 200 large ships of the line with over 2,600 attack craft total. The various fleets we seen have numbers consist of a1-3 New Macross Class, 1-3 City Dome Ship, Dozen support ship from Agriculture to Factory Ships, 45+ Guantanamo Stealth carriers, 20+ Uraga Escort Battle Carriers, 120+ Northhampton Stealth Frigates, 100+ Stealth Cruisers for rough sizes.
Thats a normal fleet make up. Then he we fleets like these.
A small special task force fleet that was sent had shown on screen from a angle at least 37 NUNS ships. consisting of Northampton Class Stealth Frigates, Stealth Cruisers, Uraga Class Escort Battle Carriers, and Guantánamo Class Stealth Carriers. Since we only get a high left angle shot of the fleet its safe to assume its really double this in size for total of 70 NUNS ships rounding down for a small task force. We also know this is the 47th fleet of the Special Fleets in service and likely more than 47 fleets of this size exist.
The private military SMS Fleet had shown over 150+ see ships Fold into battle. Majority being Uraga Class Escort Battle Carriers, half that in Northampton Class Stealth Frigates, and lead by five Macross Quarters.
When encountering Chlores Meltran Fleet we are told the estimated sizes, and by the math given this fleet has 97,000 Warships with over 1,300,000 Queadluun-Rau suits. This fleet made up of Meltran Large Battleship, Meltran Assault Landing Ships, Meltran Standard Battleships, Meltran Large Frigates all lead by a single Meltran Gunboat as the capital ship. We know this lfeet was taken into NUNs itself.
We also know there is 117+ Explorer/Research Fleets lead by a SDFN Class ship followed by a small fleet of several Uraga Class Escort Battle Carriers and Northampton Class Stealth Frigates.
In Macross Delta we see the average fleet sizes of majority of NUNS worlds seemingly limit to 2-3 Guantanamo Stealth Carriers, 3-4 Uraga Escort Battle Carriers, 4-6 Northhampton Stealth Frigates, 2-6 Stealth Cruisers, and all being lead by a Macross Quarter.
Finally we see Earth defense fleet alone being stated multiple thousands of vessels across the ENTIRE orbit of Earth consisting of Guantanamo Stealth Carriers, Uraga Escort Battle Carriers, Northhampton Stealth Frigates. Not to mention 20 or so moon size Factory Satellites that help make fleets and sustain them.
XAOS Fleet alone is a private military with a confirm soon size Factory Satellite and four Macross Variable Attack Space Aircraft Carriers that stay in the Globular Cluster/Sagittarius Galaxy as support. Add in the Windermere Fleet that teams up with XAOS for a additional Sigur Berrentzs Mobile Fortress, and several more Stealth Cruisers and custom made Carriers.
This is a general idea of the NUNs fleets at play and their numbers. Which will give HELL to 40K part of the Galaxy.