Here are the key points:
The Set Up
Typically, you should be seated at your table and ready to start well before the judges declare the start of the round. However, even if you're not ready, you still get two minutes to shuffle and set up at the start of the game.
Shuffling at the Start of the Game
Many player advocate "pile shuffling". To do this, just pretend that you are dealing out all of your cards face down for a six player game. Doing this helps to separate clumps of cards in ways that traditional shuffling methods do not. Additionally, if you manage to deal out your cards evenly into six pile, you will know that you have all your cards with you. Of course, it won't help if you somehow managed to lose or forget cards in multiples of six. Some players prefer to create piles of eight or even ten. Additionally, there are alternate methods of shuffling that still allows you to count your cards easily. What you do is up to you, just know where you should be ending the pile shuffle for 60 cards.
Don't Forget Your Prizes
Forgetting to put down your prizes is one big mistake that seems to always find us at moments of mental weakness. Despite your best efforts, it can still creep up on you and earning a game loss penalty is never fun. Myself, I have gotten into the habit of dealing out my hand and my prizes before I check for mulligan. However, I know that this is technically not the correct procedure and have started to form a new habit.
After drawing my initial hand of seven, I will put my deck in the active Pokemon spot. Now, if I have a starting basic, I cannot put it down without my deck getting in the way. Thus, I will pick up the deck, put down my six prizes and place the deck in its regular spot and then play down my starting Pokemon. It takes some getting used to, but if you keep doing it you'll never forget to put down your prizes, even if you're low on thinking capacity.
Speaking of mulligan. You should avoid declaring mulligan until after your opponent puts down their active. Of course, this is typically not a big deal, but it can make a difference for some decks. Additionally, if your opponent does inquire if you have no basics, you should answer honestly and proceed to reshuffle and redraw so to not delay the set up.
During Your Opponent's Turn
I personally prefer to think about my move on my turn and watch my opponent during their turn since what I can do on my turn will change depending on their attack. It's just less thinking and less stress this way. Leave your cards on the table so that you won't be tempted to look at them and rest your hands on your lap. Remember that it’s against the rules to lower your hand of cards under the table and beyond view. Watch your opponent's turn and make sure that they don't make any mistakes (unintentionally, of course).
When you play your energy per turn, put that energy on top of your Pokemon. Wait until you are finished with your turn before you put the energy underneath your Pokemon. This way you won't forget if you have attached an energy even during long turns. Of course, make sure that all cards remain visible! If you do forget to follow this tip and forget if you had attached this turn, count the energy already on your field and try to remember the number of turns that you have already played. Alternatively, see how many energies your opponent has on the field and compare it with yours while noting who went first.
Be sure to announce your powers! A player at Canadian Nationals this year suffered for not declaring Pachirisu's Self Generation ability when he played it down with a single energy. Don't let this be you, declare Inferno Fandango and similar abilities (see Powers and Abilities section below).
Judges at Worlds gave warnings to players that left their Supporters next to their active Pokemon instead of discarding them immediately. As such, your local Battle Roads judge may be doing the same. When playing your Supporter for the turn, place it sideways in your discard pile so that it is perpendicular to the rest of the cards. Now you can tell immediately if you have played your Supporter yet for the turn with a glance! Straighten up your discard at the end of your turn.
Searching Your Deck
When searching through your deck (after using a card like Pokemon Collector, for example), do not drop down your Pokemon face up on your play mat. Instead, move the cards that you are thinking about retrieving to the top of your deck or put them face down far away from your hand and bench area (the spot above your active is a good spot). Only once you have thoroughly thought over your choices and picked out the Pokemon that you want should you reveal what you have grabbed and put them into your hand. Some players have been zinged when, after dropping down three Pokemon, their opponent did not permit them to change their mind and, in some case, forced the player to bench all three immediately and in order (which negated the use of some Powers as well).
If you want to be extra pro, take an extra second while going through your first deck search and try to identify what your prizes are. However, don't take too long! You should know your deck well enough to quickly identify what's been prized. Additionally, you can declump some cards that you do not want to be suck together, such as two Professor Junipers, for example. After searching and declumping, shuffle light so that you won't re-clump those cards back together. Of course, offer the cut to your opponent afterwards.
Keep Track of Resources
This is a bit of a higher level thing to keep in mind and has less to do with physically playing the game and more to do with the strategies and tactics of the game. You should regularly check your opponent's discard pile as well as your own (be sure to ask politely before reaching over to grab someone else' cards). Have an idea of what your opponent plays in their deck and what they might be able to do on their next turn. This is especially good in the current meta with all the Pokemon Catchers and Junk Arms flying around. Additionally, you should get into the habit of checking your opponent's hand size at the start of your turn. Not only is this useful for hand matching if you're playing a Yanmega Prime deck (or avoid the hand match if you're playing against one), but it's also good to making sure that nothing sketchy is going on. For example, if you're going first in a game, your opponent shouldn't have more than six cards in their hand unless you mulligan'd.
Powers and Abilities
The use of Pokemon Powers and Abilities is another thing that is easy to lose track of, especially when you have multiple Magnezone Primes on the field. When I was judging the eight-man pods at Worlds, I noticed that the Japanese players "tapped" the cards when they used its power. "Tapping" is a term from Magic: The Gathering and refers to when you turn the card sideways to indicate that it has been used. However, an issue can arise from this if you turn your active Pokemon sideways (which also indicates a special condition). Instead of turning the full 90 degrees, I recommend turning your Pokemon 45 degrees after using a once-per-turn ability.
Speaking of special conditions, as noted in the Rules Section, BW-on Abilities can still be used even if the Pokemon is affected by a special condition. This is, of course, unless the card itself specifically says otherwise. But none of the BW-on Abilities so far states as such.
As mentioned above, be sure to announce your powers. Normally judges won't make you say the full name every time. I personally prefer saying "power" and tapping the Pokemon whose power I'm using.
As a special aside, when using Reuniclus' Damage Swap ability. It's best to add up all the damage on your side of the field before manipulating the damage. This way you can be sure that you end up with the same amount that you started with.
Clean Up Phase
There is no actual Clean Up Phase in Pokemon. However, if you have been following the tips above, you will need to do the following at the end of every turn:
-Tidy discard pile to straighten your Supporters
-Move energies played this turn under your Pokemon
-Straighten and reset Pokemon whose powers you used this turn
-Put down your hand and watch your opponent