The Quincentennial MOD incorporates and vastly improves upon nearly every major Bridge Commander Modification to date; but is completely incompatible with all of them in their original form as they’ve been completely overhauled and are complexly interconnected.  This is a standalone Mod requiring only the Patch v 1.1 and BCMI for using the plugins.  Any other Mod installed on top of this one will result in non-functionality or, at best, many errors.  The download contains plugins that are required for selecting what type of game-mode you wish to play, the type of crew you wish to have and what era to play in.  The “Game Modes” plugins take precedence over others.  The “Select Crew” and “Select Era” plugins should be selected after if desired.  The features of this Mod are far too numerous to list but I will cover a few things concerning functionality that aren’t intuitive.  I will then give a quick overview of the Mod and some highlights.
 
Nonintuitive functionalities:

            The buttons
            Most of the buttons are only visible when applicable.  For example, the transporter menu only appears providing you have a transporter installed; if the friendly ship your targeting has a transporter installed and you don’t, you’ll be given a transport button where the transporter menu normally appears in the science menu.  Same goes for transporting troops for capturing ships; if you have a transporter installed in your ship, you will be given the buttons for capturing if you’re targeting an enemy vessel and its shields are weak enough.  Most Buttons operate in this fashion.

            Bussard Collectors
            The bussard collectors are automatically open during warp however, you can manually open them as well.  Doing this in a nebula will recharge your power reserves.

            Warp power consumption
            Traveling at warp speeds now requires energy; as it, of course, should.  The faster one travels, the more energy required.  So be aware of power settings with some ships.

            Sensor Array Emissions
            Depending on the capacity of your sensor array, specific particle emissions are available.  Muons will temporarily disrupt your targets targeting ability; Omicrons will boost your targets shields (to be used on friendlies); Tachyons will force your target to reset their shields causing them to drop for one sec. Tetryons will temporarily disable your targets energy directed weapons.  All emissions require and use energy from reserves.

            Capturing Star Systems
            This is simply accomplished by orbiting a planet in the enemy system you wish to acquire while being accompanied by a significantly sized fleet; if you’re the Borg, your one cube will be sufficient. If you capture an enemy system prior to their defense fleet arriving,the system will fall back into enemy hands upon their arrival.  You will not be able to capture the system until all enemy defenses are eradicated.

            Hyper-gates,conduits, vortices, etc…
            A button will present itself in the helm menu when one of these options is available.  In some cases, a course selection will be required to activate the function.  This can be done in the galaxy map.  Also,the “Set Course” button will only appear when needed.

            Hull Plating
            Shield-less ships utilizing alternative protection are powered the same as shields.

            Warp-core breach in progress
            In the event of an eminent core-breach, the core must be repaired to full health to avoid destruction.  You will have only one minute to accomplish this.

            Docking
            The docking system is fairly intuitive however, one might be confused when targeting a station like DS9 while piloting a Galaxy Class and noticing the “Dock and Board” button being highlighted; Obviously, the ship can’t dock in the shuttle hangers.  What this means is that, if you select “Dock and Board”, the ship will dock and you will board the station.  The ship will be safely docked in an appropriate location.

            Bajoran Wormhole
            The wormhole is now a nav-point rather than an object.  You’ll need to be within a certain distance from it for your “Wormhole Options” to function.

            Warp speed travel time
            While traveling at warp, you’ll experience one second for every day it would take to make the trip in real life.  This may seem fast however, when operating low-warp vehicles such as the pre-NX ships of the early 22ed century, you might want to go make a cup of coffee while making the trip.

            Embark Vs. Missions
            In the Main Menu, there’s an “Embark” and a “Missions” option.  “Embark” will launch a basic quick-battle setup.  “Missions” will allow you to select missions pertaining to the time period and race you’ve selected.  For example: if your part of a Star Fleet crew in the early 23ed century, you’ll have the option to experience the VEGR mission.  I have plans to provide many more missions for each game-mode in the near future.

            Annoying bridge chatter
            If you’re like me, I play the game with “Voice” unselected in the sound menu.  If you do mute it, restart the game after doing so and the dialogue boxes will not pop-up when the bridge crew tries to speak causing the music silencing that disrupts game play.

            Silent Running
            You’ll need to be a certain distance away for silent running to function.  It makes no sense that you would turn off your power and suddenly become invisible to a ship you were just engaged in combat with.

            Upgrading Ships
            The XCV-330 can be upgraded if docked with its scaffolding in the late 21st or after.
When playing the missions with the NX-01 in the mid 22ed century, some of the earlier missions are when the ship was poorly armed.  After completing the mission, you can, at any time, return to Earth and dock with the Warp 5 Complex for upgrading.
The Constitution can be upgraded if docked with its refitting facility in the early 23ed century.  If you board the Enterprise-A being mothballed at the Saturn Smithsonian Institute in the late 24th century, you can upgrade it at the Sovereign dock and all the experimental ship facilities around Mars. 
If you go to the Mars shipyards in the mid or late 24th century, you can refit your Nebula class with three variations with the Nebula docks.
If you separate the Galaxy class and end up losing either the drive or saucer section, you can dock at Mckinley station for refit.
If you're flying Voyager trying to make your way to the alpha quadrant, docking at any station along the way will allow you to upgrade your ship.
Speaking of Voyager, if you're playing the "End Game" mission, don't forget you have that fancy armor from the future.  It's deployed via the 'Separation Protocol' menu; it's the only place I could put it.

Overview:

            This Mod allowed the player to immerse themselves in one of fifteen unique time periods spanning a five century timeline from the early 20th to the late 24th.  It also allows for this game play to be carried out as several different races and human factions.

Below is a short list of features; by no means, comprehensive:

MVAM now works in all game modes and is available for craft you enter in-game
Realistic physics
Multi-targeting for all ships
Race specific transporter sounds
Ship appropriate options (no more laying mines with a shuttle)
Automatic shuttle view
Torpedo replenishment options
Many hidden ships and objects (even within the Sol System) 
Multi sensor and shield functions for certain ships
Unique galactic contents depending on era and much much more…